Method for reducing viscosity in saccharification process

ABSTRACT

The present invention relates to compositions that can be used in hydrolyzing biomass such as compositions comprising a polypeptide having glycosyl hydrolase family 61/endoglucanase activity, methods for hydrolyzing biomass material, and methods for reducing viscosity of biomass mixture using a composition comprising a polypeptide having glycosyl hydrolase family 61/endoglucanase activity.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/453,923, filed Mar. 17, 2011, which is hereby incorporated byreference in its entirety.

FIELD OF THE INVENTION

The present invention relates to compositions useful for hydrolyzingbiomass, methods of using such compositions to hydrolyze biomassmaterials, and methods for reducing viscosity of biomasssaccharification mixtures.

BACKGROUND OF THE INVENTION

Bioconversion of renewable lignocellulosic biomass to a fermentablesugar that is subsequently fermented to produce alcohol (e.g., ethanol)as an alternative to liquid fuels has attracted the intensive attentionof researchers since the 1970s, when the oil crisis occurred (Bungay, H.R., “Energy: the biomass options”. NY: Wiley; 1981; Olsson L,Hahn-Hagerdal B. Enzyme Microb Technol 1996, 18:312-31; Zaldivar, J etal., Appl Microbiol Biotechnol 2001, 56: 17-34; Galbe, M et al., ApplMicrobiol Biotechnol 2002, 59:618-28). The production of sugars fromlignocellulosic biomass materials has been known for some time, as hasthe subsequent fermentation and distillation of the sugars into ethanol.Much of the prior development occurred around the time of World War IIwhen fuels were at a premium in such countries as Germany, Japan and theSoviet Union. These early processes were primarily directed to acidhydrolysis, which were complex in engineering and design, and weretypically sensitive to small variations in the processes, such as totemperature, pressure and/or acid concentrations. A comprehensivediscussion of these early processes is found in “Production of Sugarsfrom Wood Using High-pressure Hydrogen Chloride”, Biotechnology andBioengineering, Volume XXV, at 2757-2773 (1983).

The abundant supply of petroleum in the period from World War II throughthe early 1970s slowed ethanol conversion research. However, due to theoil crisis of 1973, researchers increased their efforts to developprocesses for the utilization of wood and agricultural byproducts forthe production of ethanol. This research was especially important fordevelopment of ethanol as a gasoline additive to reduce the dependencyof the United States upon foreign oil production, to increase the octanerating of fuels, and to reduce exhaust pollutants as an environmentalmeasure.

Concurrently with the “oil crisis,” the U.S. Environmental ProtectionAgency promulgated regulations requiring reduced lead additives. Insofaras ethanol is virtually a replacement of lead, some refineries haveselected ethanol as the substitute for its capability of easyintroduction into a refinery's operation without costly capitalequipment investment.

The high pressure and high temperature gas saccharification processesdeveloped decades ago continue to be improved. New and current researchfocuses greatly on enzymatic conversion processes, which employ enzymesfrom a variety of organisms, such as mesophilic and thermophilic fungi,yeast and bacteria, degrading cellulose into fermentable sugars.Uncertainty remains with these processes, mainly on their ability to bescaled up for commercialization and on the efficiency of ethanolproduction.

Cellulose and hemicellulose are the most abundant plant materialsproduced by photosynthesis. They can be degraded for use as an energysource by numerous microorganisms, including bacteria, yeast and fungi,which produce enzymes capable of hydrolysis of the polymeric substratesto monomeric sugars (Aro et al., 2001). Organisms are often restrictivewith regard to which sugars they use, and this dictates which sugars arebest to produce during conversion. As we approach the limits ofnon-renewable resources, we recognize the enormous potential ofcellulose to become a major renewable energy resource (Krishna et al.,2001). The effective utilization of cellulose through biologicalprocesses can potentially overcome the shortage of foods, feeds, andfuels (Ohmiya et al., 1997).

Cellulases are enzymes that hydrolyze cellulose (beta-1,4-glucan or betaD-glucosidic linkages) resulting in the formation of glucose,cellobiose, cellooligosaccharides, and the like. Cellulases have beentraditionally divided into 3 major classes: endoglucanases (EC 3.2.1.4)(“EG”), exoglucanases or cellobiohydrolases (EC 3.2.1.91) (“CBH”) andbeta-glucosidases ([beta]-D-glucoside glucohydrolase; EC 3.2.1.21)(“BG”) (Knowles et al., 1987 and Shulein, 1988). Endoglucanases actmainly on the amorphous parts of the cellulose fiber, whereascellobiohydrolases are also able to degrade crystalline cellulose.

Cellulases have also been shown to be useful in degradation of cellulosebiomass to ethanol (wherein the cellulases degrade cellulose to glucose,and yeast or other microbes further ferment the glucose into ethanol),in the treatment of mechanical pulp (Pere et al., 1996), for use as afeed additive (WO 91/04673) and in grain wet milling. Separatesaccharification and fermentation is a process whereby cellulose presentin biomass, e.g., corn stover, is converted to glucose and subsequentlyyeast strains convert glucose into ethanol. Simultaneoussaccharification and fermentation is a process whereby cellulose presentin biomass, e.g., corn stover, is converted to glucose and, at the sametime and in the same reactor, yeast strains convert glucose intoethanol. Ethanol production from readily available sources of celluloseprovides a stable, renewable fuel source.

Cellulases are produced by a number of bacteria, yeast and fungi.Certain fungi produce a complete cellulase system (i.e., a wholecellulase) capable of degrading crystalline forms of cellulose. A wholecellulase, especially one that is naturally occurring, is, however, notnecessarily capable of achieving efficient degradation because it maynot include all the components/activities required for this efficiency,for example, activities from each of the CBH, EG and BG classifications.(Filho et al., 1996). It is known that individual CBH, EG, and BGcomponents alone do not bring about efficient hydrolysis, but thecombination of EG-type cellulases and CBH-type cellulases interact tomore efficiently degrade cellulose than either enzyme used alone (Wood,1985; Baker et al., 1994; and Nieves et al., 1995).

Cellulases are known in the art to be useful in the treatment oftextiles, for enhancing the cleaning ability of detergent compositions,for use as a softening agent, for improving the feel and appearance ofcotton fabrics, and the like (Kumar et al., 1997). Cellulase-containingdetergent compositions with improved cleaning performance (U.S. Pat. No.4,435,307; GB App. Nos. 2,095,275 and 2,094,826) and for use in thetreatment of fabric to improve the feel and appearance of the textile(U.S. Pat. Nos. 5,648,263, 5,691,178, and 5,776,757, and GB App. No.1,358,599), have been described.

Hence, cellulases produced in fungi and bacteria have receivedsignificant attention. In particular, fermentation of Trichoderma spp.(e.g., T. longibrachiatum or T. reesei) has been shown to produce acomplete cellulase system capable of degrading crystalline forms ofcellulose. Over the years, Trichoderma cellulase production has beenimproved by classical mutagenesis, screening, selection and developmentof highly refined, large scale inexpensive fermentation conditions.While the multi-component cellulase system of Trichoderma spp. is ableto hydrolyze cellulose to glucose, there are cellulases from othermicroorganisms, particularly bacterial strains, with differentproperties for efficient cellulose hydrolysis, and it would beadvantageous to express these proteins in a filamentous fungus forindustrial scale cellulase production. However, the results of manystudies demonstrate that the yield of expressing bacterial enzymes fromfilamentous fungi is low (Jeeves et al., 1991).

Soluble sugars such as glucose and cellobiose have many uses for theproduction of chemicals and biological products. The optimization ofcellulose hydrolysis allows for the use of less enzymes and improvedcost effectiveness for the production of soluble sugars.

An efficient conversion of lignocellulosic biomass into fermentablesugars is key to producing bioethanol in a cost-effective andenvironmentally-friendly way. To reduce energy and processing cost,particularly for distillation, the minimum ethanol concentrationproduced by a viable process should be at least 4% (w/v). Such anincreased ethanol concentration can be achieved by processing substrateshaving high dry matter of solids. However a common problem associatedwith saccharifying a high dry matter biomass is the high viscosity ofthe slurry, resulting in a slurry that is not pumpable or requires largeenergy input during handling. When dealing with handling of high solids,problems such as 1) insufficient mixing with limited mass transfer, 2)increasing concentration of inhibitors, such as acetic acid, furfural,5-hydroxymethyl furfural, phenolic lignin degradation, 3) productioninhibition, such as glucose, cellobiose, ethanol, and 4) fermentationmicroorganism viability, will occur. High viscosity limits the drysubstance level in the process, increasing energy and water consumption,reducing the separation efficiency, evaporation and heat exchange, andultimately, the ethanol yield. Reduction of viscosity is thereforebeneficial, and enzymes play a key role in breaking down thesoluble/insoluble compounds causing high viscosity.

Studies to increase solid loading and/or reduce viscosity ofsaccharification processes have taken place. For example, a number ofstudies utilized fed-batch operations in order to increase the solidslevel in the biomass substrate loading. A gravimetric mixing reactordesign was used, which allowed batch enzymatic liquefaction andhydrolysis of pretreated wheat straw at up to 40% solids concentration.This fed-batch strategy sequentially loads the biomass substrate orsubstrate plus enzymes during enzymatic hydrolysis in order to achievehydrolysis of a large amount of substrate, a relatively low viscosityduring hydrolysis, and a relatively high glucose concentration duringthe process. Alternatively, enzymatic pre-hydrolysis of alignocellulosic biomass for a period of time at the enzymes' optimumtemperature, e.g., 50° C., can be carried out to reduce the viscosity ofthe slurry, enabling pumping and stirring. The decrease in viscosityduring pre-hydrolysis makes the subsequent fermentation or SSF possible.

Despite the development of numerous approaches, there remains a need inthe art for additional ways to reduce viscosity and improve yield ofdesirable fermentable sugars.

All references cited herein, including patents, patent applications, andpublications, are incorporated by reference in their entirety.

SUMMARY OF INVENTION

The present disclosure is based, in part, on the surprising discoverythat inclusion of a certain endoglucanase enzyme (e.g., a polypeptidehaving glycosyl hydrolase family 61 (“GH61”)/endoglucanase activity,such as the T. reesei endoglucanase (“Eg4”)) in a biomasssaccharification mixture substantially reduces the viscosity of themixture. The disclosure also pertains to the inclusion of such enzyme(s)to substantially improve the saccharification and the yields ofdesirable fermentable sugars from a given biomass substrate.

Provided herein are polypeptides having glycosyl hydrolase family 61(“GH61”)/endoglucanase activity. By “GH61/endoglucanase activity” it ismeant that the polypeptide has a GH61 activity and/or an endoglucanaseactivity. In some aspects, the polypeptide is isolated. In some aspects,the polypeptide having GH61/endoglucanase activity (e.g., an isolatedpolypeptide) is a GH61 endoglucanase or an endoglucanase IV (“EG IV”)from various species, or a polypeptide corresponding to (e.g., sharinghomology with, sharing functional domains, sharing GH61 motif(s), and/orsharing conservative residues with) a GH61 endoglucanase (e.g., a T.reesei Eg4 polypeptide). Such species include Trichoderma, Humicola,Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya,Podospora, Endothia, Mucor, Cochliobolus, Pyricularia, Chrysosporium,Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus,Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger,Aspergillus oryzae, Chrysosporium lucknowense, Fusarium bactridioides,Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusariumvenenatum, Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsisaneirina, Ceriporiopsis caregiea, Ceriporiopsis gilvescens,Ceriporiopsis pannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa,Ceriporiopsis subvermispora, Coprinus cinereus, Coriolus hirsutus,Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthorathermophila, Neurospora crassa, Neurospora intermedia, Penicilliumpurpurogenum, Penicillium canescens, Penicillium solitum, Penicilliumfuniculosum Phanerochaete chrysosporium, Phlebia radiate, Pleurotuseryngii, Talaromyces flavus, Thielavia terrestris, Trametes villosa,Trametes versicolor, Trichoderma harzianum, Trichoderma koningii,Trichoderma longibrachiatum, Trichoderma reesei, Trichoderma viride,Geosmithia emersonii, or G. stearothermophilus.

In some aspects, the polypeptide having GH61/endoglucanase activity(e.g., an isolated polypeptide) is a GH61 endoglucanase selected fromthe group consisting of the polypeptides with amino acid sequences shownin FIG. 1 of the present disclosure. For example, suitable GH61endoglucanases include those that are are represented by their GenBankAccession Numbers CAB97283.2, CAD70347.1, CAD21296.1, CAE81966.1,CAF05857.1, EAA26873.1, EAA29132.1, EAA30263.1, EAA33178.1, EAA33408.1,EAA34466.1, EAA36362.1, EAA29018.1, and EAA29347.1, or those that arenamed St61 from S. thermophilum 24630, St61A from S. thermophilum23839c, St61B from S. thermophilum 46583, St61D from S. thermophilum80312, Afu61a from A. fumigatus Afu3g03870 (NCBI Ref: XP_(—)748707), anendoglucanase of NCBI Ref: XP_(—)750843.1 from A. fumigatus Afu6g09540,an endoglucanase of A. fumigatus EDP47167, an endoglucanase of T.terrestris 16380, an endoglucanase of T. terrestris 155418, anendoglucanase of T. terrestris 68900, Cg61A (EAQ86340.1) from C.globosum, T. reesei Eg7, T. reesei Eg4, and an endoglucanase withGenBank Accession: XP_(—)752040 from A. fumigatus Af293. In someaspects, the polypeptide having GH61/endoglucanase activity (e.g.,isolated polypeptide) comprises an amino acid sequence that is at leastabout 60% (e.g., at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%) sequence identity to any one ofSEQ ID NOs: 1-29 and 148. In certain aspects, the polypeptide havingGH61/endoglucanase activity (e.g., isolated polypeptide) comprises anamino acid sequence that comprises one or more sequence motif(s)selected from the group consisting of: (1) SEQ ID NOs:84 and 88; (2) SEQID NOs:85 and 88; (3) SEQ ID NO:86; (4) SEQ ID NO:87; (5) SEQ ID NOs:84,88 and 89; (6) SEQ ID NOs:85, 88, and 89; (7) SEQ ID NOs: 84, 88, and90; (8) SEQ ID NOs: 85, 88 and 90; (9) SEQ ID NOs:84, 88 and 91; (10)SEQ ID NOs: 85, 88 and 91; (11) SEQ ID NOs: 84, 88, 89 and 91; (12) SEQID NOs: 84, 88, 90 and 91; (13) SEQ ID NOs: 85, 88, 89 and 91: and (14)SEQ ID NOs: 85, 88, 90 and 91. In some embodiments, the polypeptide isat least about 100 (e.g., at least about 120, 130, 140, 150, 160, 170,180, 190, 200, 220, 240, or more) amino acid residues in length.

In some aspects, the polypeptide having GH61/endoglucanase activity is avariant of a GH61 endoglucanase such as, for example, one selected fromthose listed in FIG. 1. Suitable polypeptide include, e.g, GenBankAccession Number CAB97283.2, CAD70347.1, CAD21296.1, CAE81966.1,CAF05857.1, EAA26873.1, EAA29132.1, EAA30263.1, EAA33178.1, EAA33408.1,EAA34466.1, EAA36362.1, EAA29018.1, or EAA29347.1, or St61 of S.thermophilum 24630, St61A of S. thermophilum 23839c, St61B of S.thermophilum 46583, St61D of S. thermophilum 80312, Afu61a of A.fumigatus Afu3g03870 (NCBI Ref: XP_(—)748707), an enzyme of A. fumigatusAfu6g09540 (NCBI Ref: XP_(—)750843.1), an enzyme of A. fumigatusEDP47167, an enzyme of T. terrestris 16380, an enzyme of T. terrestris155418, an enzyme of T. terrestris 68900, and C. globosum Cg61A(EAQ86340.1), T. reesei Eg7, T. reesei Eg4, and an enzyme of A.fumigatus Af293 (with GenBank Accession: XP_(—)752040). In some aspects,the polypeptide having GH61/. endoglucanase activity is a variant of anenzyme comprising any one of SEQ ID NOs: 1-29 and 148. The polypeptidehaving GH61/endoglucanase activity may be a variant of an enzyme havingat least about 100 (e.g., at least about 110, 120, 130, 140, 150, 160,170, 180, 190, 200, 220, 240 or more) amino acid residues in length,comprising one or more of the sequence motifs selected from: (1) SEQ IDNOs:84 and 88; (2) SEQ ID NOs:85 and 88; (3) SEQ ID NO:86; (4) SEQ IDNO:87; (5) SEQ ID NOs:84, 88 and 89; (6) SEQ ID NOs:85, 88, and 89; (7)SEQ ID NOs: 84, 88, and 90; (8) SEQ ID NOs: 85, 88 and 90; (9) SEQ IDNOs:84, 88 and 91; (10) SEQ ID NOs: 85, 88 and 91; (11) SEQ ID NOs: 84,88, 89 and 91; (12) SEQ ID NOs: 84, 88, 90 and 91; (13) SEQ ID NOs: 85,88, 89 and 91: and (14) SEQ ID NOs: 85, 88, 90 and 91. The polypeptidehaving GH61/endoglucanase activity may be a variant of a GH61endoglucanase, wherein the variant has an amino acid sequence having atleast about 60% (e.g., at least about any of 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 96%, 97%, 98%, or 99%) identity to any one of SEQ IDNOs:1-18.

In some aspects, the polypeptide having GH61/endoglucanase activity(e.g., an isolated polypeptide, including a variant of GH61endoglucanase) has endoglucanase activity. The variant may comprise atleast one motif (at least 1, 2, 3, 4, 5, 6, 7, or 8 motifs) selectedfrom SEQ ID NOs:84-91. For the purpose of the present disclosure enzymescan be referred to by their functionalities. For example, aneodnglucanse polypeptide can also be referred as polypeptide havingendoglucanase activity, or vise versa.

In some aspects, the polypeptide having GH61/endoglucanase activity(including a variant of GH61 endoglucanase) comprises one or moresequence motif(s) selected from: (1) SEQ ID NOs:84 and 88; (2) SEQ IDNOs:85 and 88; (3) SEQ ID NO:86; (4) SEQ ID NO:87; (5) SEQ ID NOs:84, 88and 89; (6) SEQ ID NOs:85, 88, and 89; (7) SEQ ID NOs: 84, 88, and 90;(8) SEQ ID NOs: 85, 88 and 90; (9) SEQ ID NOs:84, 88 and 91; (10) SEQ IDNOs: 85, 88 and 91; (11) SEQ ID NOs: 84, 88, 89 and 91; (12) SEQ ID NOs:84, 88, 90 and 91; (13) SEQ ID NOs: 85, 88, 89 and 91: and (14) SEQ IDNOs: 85, 88, 90 and 91.

In some aspects, the polypeptide having GH61/endoglucanase activity(including a variant) comprises a CBM domain (e.g., functional CBMdomain). In some aspects, the polypeptide having GH61/endoglucanaseactivity (including a variant of GH61 endoglucanase) comprises acatalytic domain (e.g., functional catalytic domain).

Also provided herein are variants of EG IV polypeptides. For example,such variants can have at least about 60% (e.g., at least about 60%,65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%) sequence identity to any one of SEQ ID NOs: 1-29 and 148, or to amature polypeptide thereof. For example, provided herein are variants ofT. reesei Eg4 polypeptide. Such variants may have at least about 60%(e.g., at least about 60%, 65%, 70%, 75%, 80%, 85%, 88%, 90%, 92.5%,95%, 96%, 97%, 98%, or 99%) sequence identity to residues 22 to 344 ofSEQ ID NO:27. In some aspects, the polypeptide or a variant thereof isisolated. In some aspects, the polypeptide or a variant thereof hasendoglucanase activity. In some aspects, the polypeptide or a variantthereof comprises residues corresponding to at least about 5 residues(e.g., at least about any of 6, 7, 8, 9, 10, 11, or 12) of H22, D61,G63, C77, H107, R177, E179, H184, Q193, C198, Y195, and Y232 of SEQ IDNO:27, or any corresponding conserved residues in any of the otherpolypeptides. In some aspects, the polypeptide or a variant thereofcomprises residues corresponding to H22, D61, G63, C77, H107, R177,E179, H184, Q193, C198, Y195, and Y232 of SEQ ID NO:27. The polypeptideor a variant thereof may comprise residues corresponding to at least 5residues (e.g., at least about any of 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, or 19) of G313, Q314, C315, G316, G317, S321, G322,P323, T324, C326, A327, T331, C332, N336, Y338, Y339, Q341, C342, andL343 of SEQ ID NO:27. In some aspects, the polypeptide or a variantthereof comprises residues corresponding to G313, Q314, C315, G316,G317, 5321, G322, P323, T324, C326, A327, T331, C332, N336, Y338, Y339,Q341, C342, and L343 of SEQ ID NO:27. The polypeptide or a variantthereof may comprise a CBM domain (e.g., a functional CBM domain). Insome aspects, the polypeptide or a variant thereof comprises a catalyticdomain (e.g., a functional catalytic domain).

Also provided herein are nucleic acids or polynucleotides encoding anyone of the polypeptides herein. For example, the disclosure providespolynucleotide encoding a polypeptide having at least about 60% (e.g.,at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%) sequence identity to any one of SEQ ID NOs:1-29 and 148. For example, the disclosure provides herein isolatednucleic acids having at least about 60% (e.g., at least about 60%, 65%,70%, 75%, 80%, 85%, 88%, 90%, 92.5%, 95%, 96%, 97%, 98%, or 99%)identity to SEQ ID NO:30. Also provided are expression cassettes,vectors, and cells comprising the nucleic acids described above.

Also provided herein are enzyme compositions (e.g., non-naturallyoccurring compositions) comprising a polypeptide havingGH61/endoglucanase activity. In some aspects, the composition comprisesa whole cellulase comprising the polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof). The polypeptidehaving GH61/endoglucanase activity is, e.g., T. reesei endoglucanase IV(“T. reesei Eg4”) or a variant thereof. A variant of T. reesei Eg4 canbe any of the variants provided herein.

In some aspects, the enzyme composition is a cellulase composition. Theenzyme composition may further comprise one or more hemicellulases, andthus can also be a hemicellulase composition. In some aspects, theenzyme composition comprises at least one (e.g., at least 2, 3, 4, 5, 6,7, or 8) cellulase polypeptide(s). In some aspects, the at least onecellulase polypeptide is a polypeptide having endoglucanase activity, apolypeptide having cellobiohydrolase activity, or a polypeptide havingβ-glucosidase activity. In some aspects, the composition furthercomprises at least one (e.g., at least 2, 3, 4, 5, 6, 7, or 8)hemicellulase polypeptide(s). In some aspects, the at least onehemicellulase polypeptide is a polypeptide having xylanase activity, apolypeptide having β-xylosidase activity, or a polypeptide havingL-α-arabinofuranosidase activity, or a polypeptide having combinedxylanase/β-xylosidase activity, combinedβ-xylosidase/L-α-arabinofuranosidase activity, or combinedxylanase/L-α-arabinofuranosidase activity activity. In some aspects, thecomposition comprises at least one (e.g., at least 2, 3, 4, 5, 6, 7, or8) cellulase polypeptide(s) and at least one (e.g., at least 2, 3, 4, 5,6, 7, or 8) hemicellulase polypeptide(s).

In some aspects, the enzyme composition comprises a polypeptide havingGH61/endoglucanase activity and further comprises at least 1 (e.g., atleast 2, 3, 4, or 5) polypeptide having endoglucanase activity, at least1 (e.g., at least 2, 3, 4, or 5) polypeptide having cellobiohydrolaseactivity, at least 1 (e.g., at least 2, 3, 4, or 5) polypeptide havingβ-glucosidase activity, at least 1 (e.g., at least 2, 3, 4, or 5)polypeptide having xylanase activity, at least 1 (e.g., at least 2, 3,4, or 5) polypeptide having β-xylosidase activity, and/or at least 1(e.g., at least 2, 3, 4, or 5) polypeptide havingL-α-arabinofuranosidase activity.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one polypeptide having xylanase activity (e.g., T. reeseiXyn3, T. reesei Xyn2, AfuXyn2, AfuXyn5, or a variant thereof). In someaspects, the composition further comprises at least one polypeptidehaving β-glucosidase activity (e.g., Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B,Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, Tn3B, or a variant thereof).In some aspects, the composition further comprises at least onepolypeptide having cellobiohydrolase activity (e.g., T. reesei CBH1, A.fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris 7A, 7B, T. reeseiCBH2, T. terrestris 6A, S. thermophile 6A, 6B, or a variant thereof). Insome aspects, the composition further comprises at least one polypeptidehaving endoglucanase activity other than the GH61 enzyme (e.g., T.reesei EG1, T. reesei EG2, or a variant thereof).

The composition may comprise a polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof) and at least 1polypeptide having β-glucosidase activity (e.g., Fv3C, Pa3D, Fv3G, Fv3D,Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, Tn3B or a variantthereof). The composition may comprise a polypeptide havingGH61/endoglucanase activity and at least 1 polypeptide havingcellobiohydrolase activity (e.g., T. reesei CBH1, A. fumigatus 7A, 7B,C. globosum 7A, 7B, T. terrestris 7A, 7B, T. reesei CBH2, T. terrestris6A, S. thermophile 6A, 6B or a variant thereof). The composition maycomprise a polypeptide having GH61/endoglucanase activity, and at least1 polypeptide having endoglucanase activity (e.g., T. reesei EG1, T.reesei EG2 or a variant thereof). The composition may comprise apolypeptide having GH61/endoglucanase activity and at least 1polypeptide having β-xylosidase activity (e.g., Fv3A, Fv43A, Pf43A,Fv43D, Fv39A, Fv43E, Fo43A, Fv43B, Pa51A, Gz43A, T. reesei Bxl1 or avariant thereof). The composition may comprise a polypeptide havingGH61/endoglucanase activity and at least 1 polypeptide havingL-α-arabinofuranosidase activity (e.g., Af43A, Fv43B, Pf51A, Pa51A,Fv51A or a variant thereof).

Any one of the compositions described herein may comprise a wholecellulase. For example, a composition is provided comprising a wholecellulase comprising a polypeptide having GH61/endoglucanase activity.Alternatively, a composition is provided comprising a whole cellulaseplus a polypeptide having GH61/endoglucanase activity. In some aspects,a composition comprising a polypeptide having GH61/endoglucanaseactivity, and a polypeptide having endoglucanase activity other than thepolypeptide having GH61/endoglucanase activity, a polypeptide havingcellobiohydrolase activity, and a polypeptide having β-glucosidaseactivity is provided. The composition further comprises one or morehemicellulase polypeptides. For example, the composition may compriseone or more polypeptides having xylanase activity, one or morepolypeptides having β-xylosidase activity, and/or one or morepolypeptides having L-α-arabinofuranosidase activity. A composition maycomprise a polypeptide having GH61/endoglucanase activity, at least onepolypeptide having xylanase activity (e.g., T. reesei Xyn3, T. reeseiXyn2, AfuXyn2, AfuXyn5, or a variant thereof), and a whole cellulase. Insome aspects, a composition comprising a polypeptide havingGH61/endoglucanase activity, at least one polypeptide having xylanaseactivity (e.g., T. reesei Xyn3, T. reesei Xyn2, AfuXyn2, AfuXyn5, or avariant thereof), and at least one other polypeptide havinghemicellulase activity is provided.

In some aspects, the whole cellulase comprises at least one polypeptidehaving endoglucanase activity (e.g., T. reesei EG1, T. reesei EG2, or avariant thereof) that is not the polypeptide having GH61/endoglucanaseactivity. The whole cellulase can comprise at least one polypeptidehaving cellobiohydrolase activity (e.g., T. reesei CBH1, A. fumigatus7A, 7B, C. globosum 7A, 7B, T. terrestris 7A, 7B, T. reesei CBH2, T.terrestris 6A, S. thermophile 6A, 6B, or a variant thereof). The wholecellulase can comprise at least one polypeptide having β-glucosidaseactivity (e.g., Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A,Gz3A, Nh3A, Vd3A, Pa3G, Tn3B, or a variant thereof).

In some aspects, in any one of the compositions described herein, the atleast one polypeptide having endoglucanase activity but is not the onehaving GH61/endoglucanase activity is, e.g., T. reesei EG1 (or a variantthereof) and/or T. reesei EG2 (or a variant thereof). In some aspects,the at least one polypeptide having cellobiohydrolase activity is, e.g.,T. reesei CBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris7A, 7B, T. reesei CBH2, T. terrestris 6A, S. thermophile 6A, 6B, or avariant thereof. In some aspects, the at least one polypeptide havingβ-glucosidase activity is, e.g., Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B,Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, and/or Tn3B, or variantsthereof. In some aspects, the at least one polypeptide having xylanaseactivity is, e.g., T. reesei Xyn3, T. reesei Xyn2, AfuXyn2, and/orAfuXyn5, or variants thereof. In some aspects, the at least onepolypeptide having β-xylosidase activity is, e.g., a Group 1β-xylosidase or a Group 2 β-xylosidase, wherein the Group 1 β-xylosidasemay be Fv3A, Fv43A polypeptide, or a variant thereof, and the Group 2β-xylosidase may be Pf43A, Fv43D, Fv39A, Fv43E, Fo43A, Fv43B, Pa51A,Gz43A, T. reesei Bxl1 polypeptide, or a variant thereof. In someaspects, the at least one polypeptide having β-xylosidase activity is,e.g., Fv3A (or a variant thereof) and/or Fv43D (or a variant thereof).In some aspects, the at least one polypeptide havingL-α-arabinofuranosidase activity may be Af43A, Fv43B, Pf51A, Pa51A,and/or Fv51A, or variants thereof.

In some aspects, a composition comprising an isolated polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)is provided. In some aspects, the polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof) is expressed by ahost cell, wherein the nucleic acid encoding the polypeptide havingGH61/endoglucanase activity has been engineered into the host cell. Forexample, the polypeptide having GH61/endoglucanase activity is expressedby a host cell, and the nucleic acid encoding that polypeptide isheterologous to the host cell.

In some aspects, a composition is provided comprising a polypeptidehaving GH61/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof), and further comprising one or more cellulase polypeptidesand/or one or more hemicellulase polypeptides, wherein the cellulasepolypeptide and/or the hemicellulase polypeptide is expressed by a hostcell, and the cellulase polypeptide and/or hemicellulase polypeptide isheterologous to the host cell. In some aspects, a composition comprisinga polypeptide having GH61/endoglucanase activity and further comprisingat least one cellulase polypeptide and/or at least one hemicellulasepolypeptide is provided, and the cellulase polypeptide and/or thehemicellulase polypeptide is expressed by a host cell, and the cellulasepolypeptide and/or hemicellulase polypeptide is endogenous to the hostcell. In some aspects, the cellulase polypeptide comprises a polypeptidehaving endoglucanase activity (e.g., T. reesei EG1, T. reesei EG2, or avariant thereof) that is different from the polypeptide havingGH61/endoglucanase activity, a polypeptide having cellobiohydrolaseactivity (e.g., T. reesei CBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B,T. terrestris 7A, 7B, T. reesei CBH2, T. terrestris 6A, S. thermophile6A, 6B, or a variant thereof), or a polypeptide having β-glucosidaseactivity (e.g., Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A,Gz3A, Nh3A, Vd3A, Pa3G, Tn3B, or a variant thereof). In some aspects,the hemicellulase polypeptide comprises a polypeptide having xylanaseactivity (e.g., T. reesei Xyn3, T. reesei Xyn2, AfuXyn2, AfuXyn5, or avariant thereof), a polypeptide having β-xylosidase activity (e.g.,Fv3A, Fv43A, Pf43A, Fv43D, Fv39A, Fv43E, Fo43A, Fv43B, Pa51A, Gz43A, T.reesei Bxl1, or a variant thereof), or a polypeptide havingL-α-arabinofuranosidase activity (e.g., Af43A, Fv43B, Pf51A, Pa51A,Fv51A, or a variant thereof).

In some aspects, the composition is prepared from a fermentation broth.In some aspects, the composition is prepared from the fermentation brothof an integrated strain (e.g., H3A/Eg4, #27, as described herein in theExamples), wherein the GH61 endoglucanase gene is integrated into thegenetic materials of the host strain. In some aspects, the compositionis prepared from the fermentation broth of a strain, wherein a nucleicacid encoding a polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof) is heterologous to the host cell,wherein the GH61 endoglucanase has been, e.g., integrated into thestrain, or expressed by a vector introduced into the host strain.

Any one of the compositions or methods provided herein comprising apolypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4 or avariant thereof) may be a whole cellulase. The composition may be afermentation broth subject to minimum post-production processing (e.g.,purification, filtration, a cell kill step, and/or ultrafiltration,etc), and is used as a whole broth formulation.

In some aspects, a composition (e.g., a non-naturally occurringcomposition) is provided comprising T. reesei Eg4, T. reesei Bg11, T.reesei xyn3, Fv3A, Fv43D, and Fv51A, or respective variants thereof. Thecomposition may be a whole cellulase. The composition may be afermentation broth subject to minimum post-production processing (e.g.,filtration, purification, ultrafiltration, a cell-kill step, etc), andis thus used as a whole broth formulation. In some aspects, thecomposition comprises an isolated T. reesei Eg4 or a variant thereof. Insome aspects, the composition comprises at least one of an isolated T.reesei Bg11, an isolated T. reesei xyn3, an isolated Fv3A, an isolatedFv43D, and an isolated Fv51A. For example, any of the above-mentionedpolypeptides can be introduced into the composition by simple additionor mixing of purified or isolated polypeptides. Alternatively, thepolypeptides herein can be expressed by the host strain using suitablerecombinant techniques, and certain of the above-mentioned polypeptidesmay be overexpressed or underexpressed, as compared to theirnaturally-occurring levels in the host cell. In some aspects, genesencoding any one of the above-mentioned polypeptides can be integratedinto the host strain. In some aspects, the composition of the presentdisclosure is prepared from a fermentation broth of the host strain. Insome aspects, the composition is from the fermentation broth of anintegrated strain (e.g., H3A/Eg4, #27, as described herein in theExamples). In some embodiments, the fermentation broth is subject tominimum post-production processing, and is used as a whole brothformulation. In some aspects, the nucleic acid encoding the GH61endoglucanase is heterologous to the host cell. In some aspects, atleast one of the nucleic acids encoding T. reesei Bg11, T. reesei xyn3,Fv3A, Fv43D, or Fv51A is heterologous to the host cell expressing theGH61 endoglucanase of the invention. In some aspects, at least onenucleic acid encoding T. reesei Bg11, T. reesei xyn3, Fv3A, Fv43D, orFv51A is endogenous to the host cell expressing the GH61 endoglucanase.

The polypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4or a variant thereof) may be present in an enzyme composition or in abiomass saccharification mixture in an amount sufficient to increase theyield of fermentable sugar(s) from hydrolysis of a biomass material(e.g., by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 60%, 70%, 80%, or 90%) as compared to the yield achieved by acontrol enzyme composition or a control biomass saccharification mixturethat is comparable in terms of the types and concentrations of enzymaticor other components therein, but without the polypeptide(s) havingGH61/endoglucanase activity. The polypeptide having GH61/endoglucanaseactivity may be present in the enzyme composition or in a biomasssaccharification mixture in an amount sufficient to reduce the viscosityof the biomass saccharification mixture during hydrolysis of the biomassmaterial therein (e.g., by at least about 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) as compared to the viscosityof a control mixture that is comparable in terms of the types andconcentrations of enzymatic or other components therein, but without thepolypeptide having GH61/endoglucanase activity. In some aspects, theenzyme composition or the biomass saccharification mixture comprises atleast 1 polypeptide having endoglucanase activity, at least 1polypeptide having cellobiohydrolase activity, at least 1 polypeptidehaving β-glucosidase activity, in total amounts that are sufficient tocause hydrolysis of the biomass material to which the polypeptides comeinto contact. The enzyme composition or the biomass saccharificationmixture may further comprise at least 1 polypeptide having xylanaseactivity, at least 1 polypeptide having β-xylosidase activity, at least1 polypeptide having L-α-arabinofuranosidase activity, and/or a wholecellulase, or a mixture thereof, in total amounts that are sufficient tocause hydrolysis of the biomass material to which the polypeptides comeinto contact.

In some aspects, the polypeptide having GH61/endoglucanase activity(e.g., T. reesei Eg4 or a variant thereof) is present in an amount thatis about 0.1 wt. % to about 50 wt. % (e.g., about 0.5 wt. % to about 30wt. %, about 1 wt. % to about 20 wt. %, about 5 wt. % to about 20 wt. %,about 7 wt. % to about 20 wt. %, or about 8 to about 15 wt. %) of thetotal weight of proteins in the enzyme composition or in the biomasssaccharification mixture. For example the polypeptide havingGH61/endoglucanase activity is present in an amount that is about 8 wt.%, about 10 wt. %, or about 12 wt. % of the total weight of proteins inthe enzyme composition or in the biomass saccharification mixture. Theenzyme composition or the biomass saccharification mixture may comprisemore than one polypeptides having GH61/endoglucanase activity. Forexample, the enzyme composition or biomass saccharification mixture cancomprise a T. reesei Eg4 or a variant thereof, as well as a T. reeseiEg7 (or a variant thereof), wherein the total amount of polypeptideshaving GH61/endoglucanase (Eg4+Eg7) activity is about 0.1 wt. % to about50 wt. % (e.g., about 0.5 wt. % to about 30 wt. %, about 2 wt. % toabout 20 wt. %, about 5 wt. % to about 20 wt. %, about 7 wt. % to about20 wt. %, or about 8 wt. % to about 15 wt. %) of the total weight ofproteins in the enzyme composition or in the biomass saccharificationmixture. The polypeptide(s) having GH61/endoglucanase activity may beexpressed from polynucleotides that are heterologous or endogenous tothe host cell. Alternatively the polypeptide having GH61/endoglucanaseactivity can be introduced into the enzyme composition or the biomasssaccharification mixture in an isolated or purified form.

In some aspects, a polypeptide having cellobiohydrolase activity (e.g.,T. reesei CBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris7A, 7B, T. reesei CBH2, T. terrestris 6A, S. thermophile 6A, 6B, or avariant thereof) is present in an amount that is about 0.1 wt. % toabout 80 wt. % (e.g., about 5 wt. % to about 70 wt. %, about 10 wt. % toabout 60 wt. %, about 20 wt. % to about 50 wt. %, or about 25 wt. % toabout 50 wt. %) of the total weight of proteins in the enzymecomposition or the biomass saccharification mixture. The enzymecomposition or biomass saccharification mixture may comprise more thanone polypeptide having cellobiohydrolase activity (e.g., T. reesei CBH1,A. fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris 7A, 7B, T. reeseiCBH2, T. terrestris 6A, S. thermophile 6A, 6B, or a variant thereof),wherein the total amount of polypeptides having cellobiohydrolaseactivity is about 0.1 wt. % to about 80 wt. % (e.g., about 5 wt. % toabout 70 wt. %, about 10 wt. % to about 60 wt. %, about 20 wt. % toabout 50 wt. %, or about 25 wt. % to about 50 wt. %) of the total weightof proteins in the enzyme composition or the biomass saccharificationmixture. The polypeptide having cellobiohydrolase activity is, in someaspects, expressed from a nucleic acid heterologous or endogenous to thehost cell. In some aspects, the polypeptide having cellobiohydrolaseactivity can be introduced into the enzyme composition or biomasssaccharification mixture in an isolated or purified form.

The enzyme composition or the biomass saccharification mixture maycomprise one or more polypeptides having β-glucosidase activity (e.g.,Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A,Pa3G, Tn3B or a variant thereof), wherein the total amount ofpolypeptides having β-glucosidase activity is about 0.1 wt. % to about50 wt. % (e.g., about 1 wt. % to about 30 wt. %, about 2 wt. % to about20 wt. %, about 5 wt. % to about 20 wt. %, or about 8 wt. % to about 15wt. %) of the total weight of proteins in the enzyme composition orbiomass saccharification mixture. The polypeptide having β-glucosidaseactivity may be expressed from a nucleic acid heterologous or endogenousto the host cell. The polypeptide having β-glucosidase activity mayalternatively be introduced into the enzyme composition or biomasssaccharification mixture in an isolated or purified form.

In some aspects, the enzyme composition or biomass saccharificationmixture can comprise one or more the polypeptides having xylanaseactivity (e.g., T. reesei Xyn3, T. reesei Xyn2, AfuXyn2, AfuXyn5, or avariant thereof), wherein the total amount of polypeptides havingxylanase activity is about 0.1 wt. % to about 50 wt. % (e.g., about 1wt. % to about 40 wt. %, about 4 wt. % to about 30 wt. %, about 5 wt. %to about 20 wt. %, or about 8 wt. % to about 15 wt. %) of the totalweight of proteins in the enzyme composition or the biomasssaccharification mixture. The polypeptide having xylanase activity canbe expressed from a nucleic acid heterologous or endogenous to the hostcell. In some aspects, the polypeptide having xylanase activity can beintroduced or mixed into the enzyme composition or the biomasssaccharification mixture in an isolated or purified form.

The enzyme composition or biomass saccharification mixture may compriseone or more polypeptides having L-α-arabinofuranosidase activity (e.g.,Af43A, Fv43B, Pf51A, Pa51A, Fv51A, or a variant thereof), wherein thetotal amount of polypeptides having L-α-arabinofuranosidase activity isabout 0.1 wt. % to about 50 wt. % (e.g., about 1 wt. % to about 40 wt.%, about 2 wt. % to about 30 wt. %, about 4 wt. % to about 20 wt. %, orabout 5 wt. % to about 15 wt. %) of the total weight of proteins in theenzyme composition or the biomass saccharification mixture. Thepolypeptide having L-α-arabinofuranosidase activity may be expressedfrom a nucleic acid heterologous or endogenous to the host cell. In someaspects, the polypeptide having L-α-arabinofuranosidase activity can beintroduced or mixed into the enzyme composition or the biomasssaccharification mixture in an isolated or purified form.

The enzyme composition or the biomass saccharification mixture maycomprise one or more polypeptides having β-xylosidase activity (e.g.,Fv3A, Fv43A, Pf43A, Fv43D, Fv39A, Fv43E, Fo43A, Fv43B, Pa51A, Gz43A, T.reesei Bxl1 or a variant thereof), wherein the total amount of thepolypeptides having β-xylosidase activity is about 0.1 wt. % to about 50wt. % (e.g., about 1 wt. % to about 40 wt. %, about 4 wt. % to about 35wt. %, about 5 wt. % to about 25 wt. %, or about 5 wt. % to about 20 wt.%) of the total weight of proteins in the enzyme composition or thebiomass saccharification mixture. The polypeptide having β-xylosidaseactivity may be expressed from a nucleic acid heterologous or endogenousto the host cell. The polypeptide having β-xylosidase activity mayalternatively be introduced into the enzyme composition or the biomasssaccharification mixture in an isolated or purified form.

In some aspects, the enzyme composition provided herein may be a wholecellulase. The whole cellulase may comprise one or more polypeptideshaving endoglucanase activity (such as, e.g, T. reesei Eg4, Eg1, Eg2,Eg7, or a variant thereof) expressed from a nucleic acid heterologous orendogenous to the host cell. The whole cellulase may also comprise oneor more polypeptides having cellobiohydrolase activity (e.g., T. reeseiCBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris 7A, 7B, T.reesei CBH2, T. terrestris 6A, S. thermophile 6A, 6B, or a variantthereof) expressed from a nucleic acid heterologous or endogenous to thehost cell. The whole cellulase may further comprise one or morepolypeptide having β-glucosidase activity (e.g., Fv3C, Pa3D, Fv3G, Fv3D,Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, Tn3B, or a variantthereof) expressed from a nucleic acid heterologous or endogenous to thehost cell. The whole cellulase may be used in the form of a fermentationbroth of the host cell. The broth can be subject to minimumpost-production processing, including, e.g., filtration, purification,ultrafiltration, a cell-kill step, etc, and thus the broth may be usedfor biomass hydrolysis in a whole broth formulation.

In some aspects, the enzyme composition provided herein is capable ofconverting a biomass material into fermentable sugar(s) (e.g., glucose,xylose, arabinose, and/or cellobiose). In some aspects, the enzymecomposition is capable of achieving at least about 0.1 (e.g., 0.1 to0.4) fraction product as determined by the calcofluor assay describedherein.

In some aspects, the enzyme composition can be a cellulase compositionor a hemicellulase composition. The enzyme composition may comprise thepolypeptide having GH61/endoglucanase activity and further may compriseone or more cellulase polypeptides and/or one or more hemicellulasepolypeptides, wherein the one or more polypeptides havingGH61/endoglucanase activity and the one or more cellulase polypeptides,and/or the one or more hemicellulase polypeptides are blended into amixture before the mixture is used to contact and hydrolyze a biomasssubstrate in a biomass saccharification mixture.

In some aspects, the one or more polypeptides having GH61/endoglucanaseactivity, one or more cellulase polypeptides, and one or morehemicellulase polypeptide, are added to a biomass material, at differenttimes. For example, a polypeptide having GH61/endoglucanase activity isadded to a biomass material before, or after, a cellulase polypeptideand/or a hemicellulase polypeptide is added to the same biomassmaterial.

In some aspects, a composition of the invention comprises at least onepolypeptide having GH61/endoglucanase activity and a biomass materialin, e.g., a mixture. For example, the composition may be a hydrolysismixture, a fermentation broth/mixture, or a biomass saccharificationmixture. The mixture may comprise one or more fermentable sugar(s).

Also provided herein are methods of hydrolyzing a biomass materialcomprising contacting the biomass material with an enzyme composition(e.g., a non-naturally occurring composition) comprising a polypeptidehaving GH61/endoglucanase activity, in an amount sufficient to hydrolyzethe biomass material in the resulting biomass saccharification mixture.

Also provided herein are methods of reducing the viscosity of a biomassmixture, and/or a biomass saccharification mixture comprising contactingthe mixture with an enzyme composition (e.g., a non-naturally occurringcomposition) comprising a polypeptide having GH61/endoglucanaseactivity, which is present in the composition in an amount sufficient toreduce the viscosity of the mixture. In some aspects, the biomassmixture or the biomass saccharification mixture comprises a biomassmaterial, optionally also fermentable sugar(s), a whole cellulase and/ora composition comprising a polypeptide having cellulase activity and/ora polypeptide having hemicellulase activity. The viscosity of themixture may be reduced by at least about 5%, (e.g., at least about 5%,10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) ascompared to the viscosity of a control mixture comprising the samecomponents at the same concentrations except that the polypeptide havingGH61/endoglucanase activity is absent from the mixture. The biomassmaterial may comprise hemicellulose, cellulose, or a mixture thereof.The biomass material may comprises glucan, xylan and/or lignin, or amixture thereof.

In some aspects, the biomass material can suitably be treated orpre-treated with an acid or a base. In some aspects, the base isammonia. The method of the invention may further comprise adjusting thepH of the biomass mixture to a pH of about 4.0 to about 6.5 (e.g., pH ofabout 4.5 to about 5.5). In some aspects, the method is performed at apH of about 4.0 to about 6.5 (e.g., pH of about 4.5 to about 5.5). Insome aspects, the method is performed for about 2 h to about 7 d (e.g.,about 4 h to about 6 d, about 8 h to about 5 d, or about 8 h to about 3d). This pH adjustment can suitably be made before putting the biomassmixture in contact with the polypeptides or the enzyme compositions.

In some aspects, the biomass material is present in a saccharificationmixture in a high solids level, e.g., the biomass material in its solidstate constitutes at least about 5 wt. % to about 60 wt. % (e.g., about10 wt. % to about 50 wt. %, about 15 wt. % to about 40 wt. %, about 15wt. % to about 30 wt. %, or about 20 wt. % to about 30 wt. %) of thetotal weight of enzymes plus biomass materials in the saccharificationmixture. By the weight of the biomass material in its solid state, it ismeant the weight of the biomass material in its dry state, its dry solidstate, its natural state, or its unprocessed state, or before thebiomass is contacted with the polypeptides in the enzyme composition.Preferably the biomass material in its solid state constitutes at leastabout 15 wt. %, and even more preferably at least about 20 wt. % or 25wt. % of the total weight of enzymes plus biomass materials in thesaccharification mixture.

In some aspects, the method comprises producing fermentable sugar(s).The amount of fermentable sugar(s) may be produced at an increased levelusing the method of the invention. For example, the amount of thefermentable sugar(s) produced using the methods or the compositionsherein is increased by at least about 5% (e.g., at least about 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) ascompared to the amount of the fermentable sugar(s) produced when thesame biomass material is hydrolyzed by an enzyme composition comprisingthe same polypeptide components at the same concentrations, except thatpolypeptide having GH61/endoglucanase activity is absent.

In some aspects, the amount of the enzyme composition comprising apolypeptide having GH61/endoglucanase activity is sufficient to increasethe yield of fermentable sugar(s) by at least about 5%, (e.g., at leastabout 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or90%), as compared to the yield of fermentable sugar(s) from the samebiomass material by an enzyme composition having the same components atthe same concentrations, except that the polypeptide havingGH61/endoglucanase activity is absent. In some aspects, the amount ofthe polypeptide having GH61/endoglucanase activity in the biomasssaccharification mixture is sufficient to reduce the viscosity of themixture by at least about 5% (e.g., at least about 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) as compared to theviscosity of a control biomass saccharification mixture comprising thesame biomass and the same panel of polypeptides at the sameconcentrations, except that the polypeptide having GH61/endoglucanaseactivity is absent.

In some aspects, the amount of the composition comprising a polypeptidehaving GH61/endoglucanase activity used in a saccharification orhydrolysis process is about 0.1 mg to about 50 mg protein (e.g., about0.2 mg to about 40 mg protein, about 0.5 mg to about 30 mg protein,about 1 mg to about 20 mg protein, or about 5 mg to about 15 mg protein)per gram of cellulose, hemicellulose, or a mixture of cellulose andhemicelluloses in the biomass material. The protein amount describedherein refers to the weight of total protein in the enzyme compositionor the biomass saccharification mixture. The proteins include apolypeptide having GH61/endoglucanase activity and may include otherenzymes such as cellulase polypeptide(s) and/or hemicellulasepolypeptide(s). In some aspects, the amount of the polypeptide havingGH61/endoglucanase activity used in the hydrolysis or saccharificationprocess is about 0.2 mg to about 30 mg (e.g., about 0.2 mg to about 20mg, about 0.5 mg to about 10 mg, or about 1 mg to about 5 mg) proteinper gram of cellulose, hemicellulose, or cellulose and hemicellulosescontained in the biomass material.

The enzyme composition or biomass saccharification mixture comprising apolypeptide having GH61/endoglucanase activity and at least 1polypeptide having endoglucanase activity (e.g., T. reesei Eg1, T.reesei Eg2, and/or a variant thereof) in the hybrolysis orsaccharification process may contain about 0.2 mg to about 30 mg (e.g.,about 0.2 mg to about 20 mg, about 0.5 mg to about 10 mg, or about 1 mgto about 5 mg) protein per gram of cellulose, hemicellulose, orcellulose and hemicellulose in the biomass material.

The enzyme composition or biomass saccharification mixture comprising apolypeptide having GH61/endoglucanase activity and at least 1polypeptide having cellobiohydrolase activity (e.g., T. reesei CBH1, A.fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris 7A, 7B, T. reeseiCBH2, T. terrestris 6A, S. thermophile 6A, 6B, or a variant thereof) inthe hydrolysis or saccharification process may contain about 0.2 mg toabout 30 mg (e.g., about 0.2 mg to about 20 mg, about 0.5 mg to about 10mg, or about 1 mg to about 5 mg) protein per gram of cellulose,hemicellulose, or cellulose and hemicellulose in the biomass material.

In some aspects, the enzyme composition or biomass saccharificationmixture comprising a polypeptide having GH61/endoglucanase activity andat least 1 polypeptide having β-glucosidase activity (e.g., Fv3C, Pa3D,Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, Tn3B,or a variant thereof) in the hydrolysis or saccharification process maycontain about 0.2 mg to about 30 mg (e.g., about 0.2 mg to about 20 mg,about 0.5 mg to about 10 mg, or about 0.5 mg to about 5 mg) protein pergram of cellulose, hemicellulose, or cellulose and hemicellulose in thebiomass material.

The enzyme composition or biomass saccharification mixture comprising apolypeptide having GH61/endoglucanase activity and at least 1polypeptide having xylanase activity (e.g., T. reesei Xyn3, T. reeseiXyn2, AfuXyn2, AfuXyn5 or a variant thereof) in the hydrolysis orsaccharification process may contain about 0.2 mg to about 30 mg (e.g.,about 0.2 mg to about 20 mg, about 0.5 mg to about 10 mg, about 0.5 mgto about 5 mg) protein per gram of cellulose, hemicellulose, orcellulose and hemicellulose in the biomass material.

The enzyme composition or the biomass saccharification mixturecomprising a polypeptide having GH61/endoglucanase activity and at least1 polypeptide having β-xylosidase activity (e.g., Fv3A, Fv43A, Pf43A,Fv43D, Fv39A, Fv43E, Fo43A, Fv43B, Pa51A, Gz43A, T. reesei Bxl1, and/ora variant thereof) used in the hydrolysis or saccharification processmay contain about 0.2 mg to about 30 mg (e.g., about 0.2 mg to about 20mg, about 0.5 mg to about 10 mg, or about 0.5 mg to about 5 mg) proteinper gram of cellulose, hemicellulose, or cellulose and hemicellulose inthe biomass material.

The enzyme composition or the biomass saccharification mixturecomprising a polypeptide having GH61/endoglucanase activity and at least1 polypeptide having L-α-arabinofuranosidase activity (e.g., Af43A,Fv43B, Pf51A, Pa51A, Fv51A, and/or a variant thereof) used in thehydrolysis or saccharification process may contain about 0.2 mg to about30 mg (e.g., about 0.2 mg to about 20 mg, about 0.5 mg to about 10 mg,or about 0.5 mg to about 5 mg) protein per gram of cellulose,hemicellulose, or cellulose and hemicellulose in the biomass material.

In some aspects, the method of the invention is performed at atemperature of about 30° C. to about 65° C. (e.g., about 35° C. to about60° C., about 40° C. to about 60° C., or about 45° C. to about 55° C.).

The method of the invention may further comprise the step of contactingthe biomass material with an enzyme composition comprising a wholecellulase. In some aspects, the step of further contacting the biomassmaterial with a composition comprising a whole cellulase is performedbefore, after, or concurrently with contacting the biomass material withan enzyme composition comprising a polypeptide having GH61/endoglucanaseactivity.

In some aspects, the method of the invention further comprises the stepcontacting the biomass material with an enzyme composition comprising apolypeptide having cellulase activity and/or a polypeptide havinghemicellulase activity. The step of contacting the biomass material witha composition comprising a polypeptide having cellulase activity and/ora polypeptide having hemicellulase activity may be performed before,after, or concurrently with contacting the biomass material with anenzyme composition comprising a polypeptide having GH61/endoglucanaseactivity.

In some aspect, the composition comprises the polypeptide havingGH61/endoglucanase activity and further comprises at least 1 cellulasepolypeptide and/or at least one hemicellulase polypeptide, wherein thepolypeptide having GH61/endoglucanase activity and at least onecellulase polypeptide and/or at least 1 hemicellulase polypeptide areblended into a mixture before the mixture is used to contact the biomassmaterial.

In some aspects, the composition comprises the polypeptide havingGH61/endoglucanase activity and further comprises 1 or more cellulasepolypeptides and/or 1 or more hemicellulase polypeptides, wherein thepolypeptide having GH61/endoglucanase activity and 1 or more cellulasepolypeptides and/or 1 or more hemicellulase polypeptides are added tothe biomass material at different times. For example, the polypeptidehaving GH61/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof) is added before or after the 1 or more cellulase polypeptidesand/or the 1 or more hemicellulase polypeptides are added.

In some aspects, methods of applying the invention in both an industrialsetting and/or a commercial setting are contemplated. Accordingly amethod or a method of manufacturing, marketing, or otherwisecommercializing the instant compositions comprising suitable GH61endoglucanases is within the purview of the disclosure. The methodincludes, for example, the application of the compositions or the GH61endoglucanase polypeptides or variants thereof in a merchant enzymesupply model, wherein the enzymes and variants, as well as thecompositions of the invention are supplied or sold to cellulosic sugarproducers, certain ethanol (bioethanol) refineries or other bio-chemicalor bio-material manufacturers. The method can also be, in some aspects,the application of the compositions or the GH61 endoglucanasepolypeptides or variants thereof in an on-site bio-refinery model,wherein the polypeptides or variants, or the non-naturally occurringcellulase and hemicellulase compositions of the invention are producedin an enzyme production system that is built by the enzyme manufacturerat a site that is located at or in the vicinity of the cellulosic sugarplant, bioethanol refineries or the bio-chemical/biomaterialmanufacturers. In some aspects, suitable biomass substrates, preferablysubject to appropriate pretreatments as described herein, can behydrolyzed using the saccharification methods and the enzymes and/orenzyme compositions herein at or near the bioethanol refineries or thebio-chemical/biomaterial manufacturing facilities. The resultingfermentable sugars can then be subject to fermentation at the samefacilities or at facilities in the vicinity.

It is to be understood that one, some, or all of the properties of theembodiments described herein may be combined to form other embodimentsof the present invention. These and other aspects of the invention willbecome apparent to one of skill in the art.

BRIEF DESCRIPTION OF THE FIGURES

The skilled artisan will understand that the drawings are forillustration purposes only and are not intended to limit the scope ofthe present teachings in anyway.

FIG. 1: depicts certain amino acid sequences of various polypeptideshaving GH61/endoglucanase activity.

FIG. 2: depicts percent identity and divergence using ClustalV (PAM250)comparing a number of amino acid sequences of various polypeptideshaving GH61/endoglucanase activity, such as those presented in FIG. 1(SEQ ID NOs: 1-28).

FIG. 3: depicts the alignment of various polypeptides havingGH61/endoglucanase activity such as those presented in FIG. 1 (SEQ IDNOs: 1-28).

FIGS. 4A-4B: FIG. 4A depicts nucleotide sequence of T. reesei Eg4 (SEQID NO:30). FIG. 4B depicts amino acid sequence of T. reesei Eg4 (SEQ IDNO:27). The predicted signal sequence is underlined, the predictedconserved domains are in bold, and the predicted linker is in italic.

FIG. 5: depicts an amino acid sequence alignment of T. reesei Eg4(TrEG4) (SEQ ID NO:27) with T. reesei Eg7 (TrEG7, or TrEGb) (SEQ IDNO:26) and TtEG (SEQ ID NO:29).

FIGS. 6A-6B: FIG. 6A provides conserved residues of T. reesei Eg4(TrEg4), inferred from sequence alignment and the known structures ofTrEG7 (crystal structure at Protein Data Bank Accession: pdb:2vtc) andTtEG (crystal structure at Protein Data Bank Accession: pdb:3EII). FIG.6B provides conserved CBM domain residues inferred from sequencealignment with known sequences of Tr6A, and Tr7A.

FIG. 7 lists a number of amino acid sequence motifs of GH61endoglucanases. Each of the “a”s in the sequence motifs represents anamino acid that may be any one of alanine, arginine, asparagine,aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine,isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine,threonine, tryptophan, tyrosine, or valine.

FIGS. 8A-8I: FIG. 8A depicts pENTR-TOPO-Bgl1-943/942 plasmid. FIG. 8Bdepicts pTrex3g 943/942 expression vector. FIG. 8C depicts pENTR/T.reesei Xyn3 plasmid. FIG. 8D depicts pTrex3g/T. reesei Xyn3 expressionvector. FIG. 8E depicts pENTR-Fv3A plasmid. FIG. 8F depicts the pTrex6gplasmid. FIG. 8G depicts pTrex6g/Fv3A expression vector. FIG. 8H depictsTOPO Blunt/Pegl1-Fv43D plasmid. FIG. 8I depicts TOPO Blunt/Pegl1-Fv51Aplasmid.

FIG. 9: provides the enzyme composition of T. reesei integrated strainH3A.

FIG. 10: lists the enzymes (purified or unpurified) that wereindividually added to each of the samples in Example 2, and the stockprotein concentrations of these enzymes.

FIG. 11A-11D: FIG. 11A depicts glucose release followingsaccharification of dilute ammonia pretreated corncob by adding enzymecompositions comprising various purified or non-purified enzymes of FIG.10, which were added to T. reesei integrated strain H3A, in accordancewith Example 2. FIG. 11B depicts cellobiose release followingsaccharification of dilute ammonia pretreated corncob by adding enzymecompositions comprising various purified or non-purified enzymes of FIG.10, which were added to T. reesei integrated strain H3A, in accordancewith Example 2; FIG. 11C depicts xylobiose release followingsaccharification of dilute ammonia pretreated corncob by adding enzymecompositions comprising various purified or non-purified enzymes of FIG.10, which were added to T. reesei integrated strain H3A, in accordancewith Example 2; FIG. 11D depicts xylose release followingsaccharification of dilute ammonia pretreated corncob by adding enzymecompositions comprising various purified or non-purified enzymes of FIG.10, which were added to T. reesei integrated strain H3A, in accordancewith Example 2.

FIGS. 12A-12B: FIG. 12A depicts the expression cassette Pegl1-eg4-sucA,as described in Example 3; FIG. 12B depicts the plasmid map of pCR BluntII TOPO containing expression cassette pEG1-EG4-sucA, as described inExample 3.

FIG. 13: depicts the amount or percentage of glucan and xylan conversionto cellobiose, glucose, xylobiose and xylose by an enzyme compositioncomprising enzymes produced by the T. reesei integrated strain H3Atransformants expressing T. reesei Eg4, in accordance with Example 3.

FIG. 14: depicts the increased percent glucan conversion observed usingan increasing amount of an enzyme composition produced by H3Atransformants expressing T. reesei Eg4. The experimental details aredescribed in Example 3.

FIG. 15: provides a T. reesei Eg4 dosing chart for Example 4 (experiment1). The sample “#27” is an H3A/Eg4 integrated strain as described inExample 4. The amounts of purified T. reesei Eg4 that were added werelisted under “Sample Description” either by wt. % or by mass (in mgprotein/g G+X).

FIGS. 16A-16B: FIG. 16A depicts the effect of T. reesei Eg4 on glucoserelease in saccharification of dilute ammonia pretreated corncobaccording to Example 4. FIG. 16B depicts the effect of T. reesei Eg4 onxylose release in saccharification of dilute ammonia pretreated corncob.The Y-axes of these figures refer to the concentrations of glucose orxylose released in the reaction mixtures. The X axes list thenames/brief descriptions of the enzyme composition samples. This isaccording to Example 4 (experiment 1).

FIGS. 17A-17B: FIG. 17A provides another T. reesei Eg4 dosing chart forExample 4 (experiment 2). The samples are described similarly to thosein FIG. 15. The amounts of purified T. reesei Eg4 that were added variedby smaller increments than those of Example 4, experiment 1 (above).FIG. 17B provides another T. reesei Eg4 dosing chart for Example 4(experiment 3). The samples are described similarly to those in FIGS. 16and 17A. The amounts of purified T. reesei Eg4 that were added varied byeven finer increments than those of Example 4, experiments 1 and 2(above)

FIGS. 18A-18B: FIG. 18A depicts the effect of T. reesei Eg4 in variousamounts (0.05 mg/g to 1.0 mg/g) on glucose release from saccharificationof dilute ammonia pretreated corncob, as described in Example 4. FIG.18B depicts the effect of T. reesei Eg4 in various amounts (0.1 mg/g to0.5 mg/g) on glucose release from saccharification of dilute ammoniapretreated corncob, as described in Example 4.

FIG. 19: depicts the effect of T. reesei Eg4 in an enzyme composition onglucose/xylose release from saccharification of different solid loadingsof dilute ammonia pretreated corn stover, as described in Example 5. Thesolid loading is listed on the x-axis as #%.

FIG. 20: provides percentage yield of xylose monomers released fromdilute ammonia pretreated corncob using an enzyme composition comprisingT. reesei Eg4, in accordance with Example 6.

FIG. 21: provides percentage yield of glucose monomer released fromdilute ammonia pretreated corncob using an enzyme composition comprisingT. reesei Eg4, in accordance with Example 6.

FIG. 22: provides yield (mg/ml) of total fermentable monomers releasedfrom dilute ammonia pretreated corncob using an enzyme compositioncomprising T. reesei Eg4, in accordance with Example 6.

FIG. 23: compares the amounts of glucose released as a result ofhydrolysis by an enzyme composition without T. reesei Eg4 vs. onecomprising T. reesei Eg4 at 0.53 mg/g. The experiment is described inExample 7.

FIG. 24: depicts the glucose monomer release as a result of treatingammonia pretreated corncob using purified T. reesei Eg4 alone, accordingto Example 7.

FIG. 25: depicts and compares the saccharification performance of theenzyme compositions produced by the T. reesei integrated strain H3A andthe integrated strain H3A/Eg4 (strain #27), at an enzyme dosage of 14mg/g. This is according to the description of Example 8.

FIG. 26: depicts the saccharification performance of the enzymecompositions produced by the T. reesei integrated strain H3A and theintegrated strain H3A/Eg4 (strain #27), at various enzyme dosages, onacid pretreated corn stover. This is according to the description ofExample 9.

FIG. 27: depicts the saccharification performance of the enzymecompositions produced by the T. reesei integrated strain H3A and theintegrated strain H3A/Eg4 (strain #27) on dilute ammonia pretreated cornleaves, stalks, or cobs, according to Example 10.

FIG. 28: compares saccharification performance, in terms the amounts ofglucose or xylose released, of enzyme compositions produced by the T.reesei integrated strain H3A and the integrated strain H3A/Eg4 (strain#27). This is according to Example 11.

FIG. 29: depicts the change in percent glucan and xylan conversion atincreasing amounts of an enzyme composition produced by the T. reeseiintegrated strain H3A/Eg4 (strain #27). This is in accordance with thedescription of Example 12.

FIG. 30: is a table listing the effect of T. reesei Eg4 addition ondilute ammonia pretreated corncob saccharification. Experimentalconditions are described in Example 13.

FIG. 31: depicts CMC hydrolysis by T. reesei Eg4. Experimentalconditions are described in Example 13.

FIG. 32: depicts cellobiose hydrolysis by T. reesei Eg4. Experimentalconditions are described in Example 13.

FIG. 33: depicts amounts for various enzyme compositions forsaccharification. Experimental conditions are described in Example 14.

FIG. 34: depicts the amount of glucose, glucose+cellobiose, or xyloseproduced with each enzyme composition corresponding to FIG. 33.Experimental conditions are described in Example 14.

FIG. 35: depicts various ratios of CBH1, CBH2 and T. reesei Eg2mixtures, as described in Example 15.

FIG. 36: depicts glucan conversion (%) using various enzymecompositions. Experimental conditions are described in Example 15.

FIG. 37 depicts the effect of ascorbic acid when a compositioncomprising T. reesei Eg4 is used to treat Avicel in the presence orabsence of CBH I, according to Example 22.

FIG. 38: depicts the effect of ascorbic acid on a composition comprisingT. reesei Eg4 is used to treat Avicel in the presence/absence of CBH II,according to Example 22

FIGS. 39A-39B: FIG. 39A depicts the amount of substrate and variousenzymes used in the experiment of Example 22, with the result depictedin FIG. 37. FIG. 39B depicts the amount of substrate and various enzymesused in the experiment of Example 22, with the result depicted in FIG.38.

FIG. 40: depicts glucose production from corncob hydrolysis usingvarious enzyme compositions, in accordance with the experimentsdescribed in Example 16.

FIG. 41: depicts xylose production from corncob hydrolysis using variousenzyme compositions in accordance with the description of Example 16.

FIG. 42: depicts viscosity of saccharification mixture using H3A and H3Aadded with purified Eg4 over time in accordance with the description ofExample 17.

FIG. 43: depicts viscosity of saccharification mixture using H3A andH3A/Eg4#27 over time in accordance with the description of Example 18.

FIG. 44: depicts viscosity of saccharification of dilute ammoniapretreated corncob at 25% and 30% solids, using fermentation broths ofH3A or of H3A/Eg4#27 broth at 14 mg/g cellulose, in accordance with thedescription of Example 19.

FIG. 45: depicts glucose concentration in 6-h saccharification, 25% drymatter, 50° C., pH5.0 using various enzyme compositions according toExample 20.

FIG. 46: depicts glucose concentration in 24-hour saccharification, 25%dry matter, 50° C., pH5.0 using various enzyme compositions according toExample 20.

FIG. 47: depicts glucose concentration in saccharification over time,25% dry matter, 50° C., pH5.0 using various enzyme compositionsaccording to Example 20.

FIG. 48: depicts glucan conversion in saccharification over time, 25%dry matter, 50° C., pH5.0 using various enzyme compositions according toExample 20.

FIG. 49 provides a summary of the sequence identifies in the presentdisclosure.

FIGS. 50A-50B: FIG. 50A depicts nucleotide sequence encoding Fv3A (SEQID NO:35). FIG. 50B depicts Fv3A amino acid sequence (SEQ ID NO:36). Thepredicted signal sequence is underlined, and the predicted conserveddomain is in bold.

FIGS. 51A-51B: FIG. 51A depicts nucleotide sequence encoding Pf43A (SEQID NO:37). FIG. 51B depicts Pf43A amino acid sequence (SEQ ID NO:38).The predicted signal sequence is underlined, the predicted conserveddomain is in bold, the predicted carbohydrate binding module (“CBM”) isin uppercase, and the predicted linker separating the CD and CBM is initalics.

FIG. 52A-52B: FIG. 52A depicts nucleotide sequence encoding Fv43E (SEQID NO:39). FIG. 52B depicts Fv43E amino acid sequence (SEQ ID NO:40).The predicted signal sequence is underlined, and the predicted conserveddomain is in bold.

FIGS. 53A-53B: FIG. 53A depicts nucleotide sequence encoding Fv39A (SEQID NO:41). FIG. 53B depicts Fv39A amino acid sequence (SEQ ID NO:42).The predicted signal sequence is underlined, and the predicted conserveddomain is in bold.

FIGS. 54A-54B: FIG. 54A depicts nucleotide sequence encoding Fv43A (SEQID NO:43). FIG. 54B depicts Fv43A amino acid sequence (SEQ ID NO:44).The predicted signal sequence is underlined, the predicted conserveddomain in bold, the predicted CBM in uppercase, and the predicted linkerconnecting the conserved domain and CBM in italics.

FIGS. 55A-55B: FIG. 55A depicts nucleotide sequence encoding Fv43B (SEQID NO:45). FIG. 55B depicts Fv43B amino acid sequence (SEQ ID NO:46).The predicted signal sequence is underlined. The predicted conserveddomain is in boldface type.

FIGS. 56A-56B: FIG. 56A depicts nucleotide sequence encoding Pa51A (SEQID NO:47). FIG. 56B depicts Pa51A amino acid sequence (SEQ ID NO:48).The predicted signal sequence is underlined. The predictedL-α-arabinofuranosidase conserved domain is in bold. For expression inT. reesei, the genomic DNA was codon optimized (see FIG. 73C).

FIGS. 57A-57B: FIG. 57A depicts nucleotide sequence encoding Gz43A (SEQID NO:49). FIG. 57B depicts Gz43A amino acid sequence (SEQ ID NO:50).The predicted signal sequence is underlined, and the predicted conserveddomain is in bold. For expression in T. reesei, the predicted signalsequence was replaced by T. reesei CBH1 signal sequence(myrklavisaflatara (SEQ ID NO: 120)).

FIGS. 58A-58B: FIG. 58A depicts nucleotide sequence encoding Fo43A (SEQID NO:51). FIG. 58B depicts Fo43A amino acid sequence (SEQ ID NO:52).The predicted signal sequence is underlined, and the predicted conserveddomain is in bold. For expression in T. reesei, the predicted signalsequence was replaced by T. reesei CBH1 signal sequence(myrklavisaflatara (SEQ ID NO:120))

FIGS. 59A-59B: FIG. 59A depicts nucleotide sequence encoding Af43A (SEQID NO:53). FIG. 59B depicts Af43A amino acid sequence (SEQ ID NO:54).The predicted conserved domain is in bold.

FIGS. 60A-60B: FIG. 60A depicts nucleotide sequence encoding Pf51A (SEQID NO:55). FIG. 60B depicts Pf51A amino acid sequence (SEQ ID NO:56).The predicted signal sequence is underlined, and the predictedL-α-arabinofuranosidase conserved domain in bold. For expression in T.reesei, the predicted signal sequence was replaced by a codon optimizedthe T. reesei CBH1 signal sequence (myrklavisaflatara (SEQ ID NO:120))(underlined) and the Pf51A nucleotide sequence was codon optimized forexpression.

FIGS. 61A-61B: FIG. 61A depicts nucleotide sequence encoding AfuXyn2(SEQ ID NO:57). FIG. 61B depicts AfuXyn2 amino acid sequence (SEQ IDNO:58). The predicted signal sequence is underlined, and the predictedGH11 conserved domain in bold.

FIGS. 62A-62B: FIG. 62A depicts nucleotide sequence encoding AfuXyn5(SEQ ID NO:59). FIG. 62B depicts AfuXyn5 amino acid sequence (SEQ IDNO:60). The predicted signal sequence is underlined, and the predictedGH11 conserved domain in bold.

FIGS. 63A-63B: FIG. 63A depicts nucleotide sequence encoding Fv43D (SEQID NO:61). FIG. 63B depicts Fv43D amino acid sequence (SEQ ID NO:62).The predicted signal sequence is underlined. The predicted conserveddomain is in bold.

FIGS. 64A-64B: FIG. 64A depicts nucleotide sequence encoding Pf43B (SEQID NO:63). FIG. 64B depicts Pf43B amino acid sequence (SEQ ID NO:64).The predicted signal sequence is underlined, and the predicted conserveddomain is in bold.

FIGS. 65A-65B: FIG. 65A depicts nucleotide sequence encoding Fv51A (SEQID NO:65). FIG. 65B depicts Fv51A amino acid sequence (SEQ ID NO:66).The predicted signal sequence is underlined, and the predictedL-α-arabinofuranosidase conserved domain is in bold.

FIGS. 66A-66B: FIG. 66A depicts nucleotide sequence encoding Cg51B (SEQID NO:67). FIG. 66B depicts Cg51B amino acid sequence (SEQ ID NO:68).The predicted signal sequence corresponding is underlined, and thepredicted conserved domain is in bold.

FIGS. 67A-67B: FIG. 67A depicts nucleotide sequence encoding Fv43C (SEQID NO:69). FIG. 67B depicts Fv43C amino acid sequence (SEQ ID NO:70).The predicted signal sequence is underlined, and the predicted conserveddomain is in bold.

FIGS. 68A-68B: FIG. 68A depicts nucleotide sequence encoding Fv30A (SEQID NO:71). FIG. 68B depicts Fv30A amino acid sequence (SEQ ID NO:72).The predicted signal sequence is underlined.

FIGS. 69A-69B: FIG. 69A depicts nucleotide sequence encoding Fv43F (SEQID NO:73). FIG. 69B depicts Fv43F amino acid sequence (SEQ ID NO:74).The predicted signal sequence is underlined.

FIGS. 70A-70B: FIG. 70A depicts nucleotide sequence encoding T. reeseiXyn3 (SEQ ID NO:75). FIG. 70B depicts Xyn3 amino acid sequence (SEQ IDNO:76). The predicted signal sequence is underlined, and the predictedconserved domain is in bold.

FIGS. 71A-71B: FIG. 71A depicts amino acid sequence of T. reesei Xyn2(SEQ ID NO:77). The signal sequence is underlined. The predictedconserved domain is in bold. The coding sequence can be found inTörrönen et al. Biotechnology, 1992, 10:1461-65. FIG. 71B depicts thenucleotide sequence encoding Xyn2 (SEQ ID NO:160).

FIGS. 72A-72B: FIG. 72A depicts amino acid sequence of T. reesei Bxl1(SEQ ID NO:78). The signal sequence is underlined. The predictedconserved domain is in bold. The coding sequence can be found inMargolles-Clark et al. Appl. Environ. Microbiol. 1996, 62(10):3840-46.FIG. 72B depicts nucleotide sequence encoding Bxl1 (SEQ ID NO: 159)

FIGS. 73A-73F: FIG. 73A depicts amino acid sequence of T. reesei Bgl1(SEQ ID NO:79). The signal sequence is underlined. The predictedconserved domain is in bold. The coding sequence can be found in Barnettet al. Bio-Technology, 1991, 9(6):562-567. FIG. 73B depicts deduced cDNAfor Pa51A (SEQ ID NO:80). FIG. 73C depicts codon optimized cDNA forPa51A (SEQ ID NO:81). FIG. 73D: depicts coding sequence for a constructcomprising a CBH1 signal sequence (underlined) upstream of genomic DNAencoding mature Gz43A (SEQ ID NO:82). FIG. 73E: depicts coding sequencefor a construct comprising a CBH1 signal sequence (underlined) upstreamof genomic DNA encoding mature Fo43A (SEQ ID NO:83). FIG. 73F: depictscodon optimized coding sequence for a construct comprising a CBH1 signalsequence (underlined) upstream of codon optimized DNA encoding maturePf51A (SEQ ID NO:92).

FIGS. 74A-74B: FIG. 74A depicts nucleotide sequence encoding Pa3D (SEQID NO:93). FIG. 74B depicts amino acid sequence of Pa3D (SEQ ID NO:94).The predicted signal sequence is underlined, and the predicted conserveddomains are in bold.

FIGS. 75A-75B: FIG. 75A depicts nucleotide sequence encoding Fv3G (SEQID NO:95). FIG. 75B depicts amino acid sequence of Fv3G (SEQ ID NO:96).The predicted signal sequence is underlined, and the predicted conserveddomains are in bold.

FIGS. 76A-76B: FIG. 76A depicts nucleotide sequence encoding Fv3D (SEQID NO:97). FIG. 76B depicts amino acid sequence of Fv3D (SEQ ID NO:98).The predicted signal sequence is underlined, and the predicted conserveddomains are in bold.

FIGS. 77A-77B: FIG. 77A depicts nucleotide sequence encoding Fv3C (SEQID NO:99). FIG. 77B depicts amino acid sequence of Fv3C (SEQ ID NO:100).The predicted signal sequence is underlined, and the predicted conserveddomains are in bold.

FIGS. 78A-78B: FIG. 78A depicts nucleotide sequence encoding Tr3A (SEQID NO:101). FIG. 78B depicts amino acid sequence of Tr3A (SEQ IDNO:102). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 79A-79B: FIG. 79A depicts nucleotide sequence encoding Tr3B (SEQID NO:103). FIG. 79B depicts amino acid sequence of Tr3B (SEQ IDNO:104). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 80A-80B: FIG. 80A depicts nucleotide sequence encoding Te3A (SEQID NO:105). FIG. 80B depicts amino acid sequence of Te3A (SEQ IDNO:106). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 81A-81B: FIG. 81A depicts nucleotide sequence encoding An3A (SEQID NO:107). FIG. 81B depicts amino acid sequence of An3A (SEQ IDNO:108). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 82A-82B: FIG. 82A depicts nucleotide sequence encoding Fo3A (SEQID NO:109). FIG. 82B depicts amino acid sequence of Fo3A (SEQ IDNO:110). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 83A-83B: FIG. 83A depicts nucleotide sequence encoding Gz3A (SEQID NO:111). FIG. 83B depicts amino acid sequence of Gz3A (SEQ IDNO:112). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 84A-84B: FIG. 84A depicts nucleotide sequence encoding Nh3A (SEQID NO:113). FIG. 84B depicts amino acid sequence of Nh3A (SEQ IDNO:114). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 85A-85B: FIG. 85A depicts nucleotide sequence encoding Vd3A (SEQID NO:115). FIG. 85B depicts amino acid sequence of Vd3A (SEQ IDNO:116). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIGS. 86A-86B: FIG. 86A depicts nucleotide sequence encoding Pa3G (SEQID NO:117). FIG. 86B depicts amino acid sequence of Pa3G (SEQ IDNO:118). The predicted signal sequence is underlined, and the predictedconserved domains are in bold.

FIG. 87: depicts amino acid sequence encoding Tn3B (SEQ ID NO:119). Thestandard signal prediction program, Signal P(www.cbs.dtu.dk/services/SignalP/) provided no predicted signal.

FIG. 88: depicts a partial amino acid sequence alignment of the CBMdomains of T. reesei Eg4 (SEQ ID NO:27) with Tr6A (SEQ ID NO:31) andwith Tr7A (SEQ ID NO:32).

FIGS. 89A-89C: FIG. 89A depicts amino acid sequence of Eg6 (SEQ IDNO:33) from T. reesei. The bolded amino acid sequence is the predictedsignal peptide sequence. FIG. 89B depicts amino acid sequence of S.coccosporum endoglucanase SEQ ID NO:34; FIG. 89C depicts the nucleotidesequence encoding a GH61A from Thermoascus aurantiacus, SEQ ID NO:149.

FIGS. 90A-90I: FIG. 90A depicts amino acid sequence of Afu7A (SEQ IDNO:150), a homolog of CBH1 of T. reesei. FIG. 90B depicts amino acidsequence of Afu7B (SEQ ID NO:151), a homolog of CBH1 of T. reesei. FIG.90C depicts amino acid sequence of Cg7A (SEQ ID NO:152), a homolog ofCBH1 of T. reesei. FIG. 90D depicts amino acid sequence of Cg7B (SEQ IDNO:153), a homolog of CBH1 of T. reesei. FIG. 90E depicts amino acidsequence of Tt7A (SEQ ID NO:154), a homolog of CBH1 of T. reesei. FIG.90F depicts amino acid sequence of Tt7B (SEQ ID NO:155), a homolog ofCBH1 of T. reesei. FIG. 90G depicts amino acid sequence of St6A (SEQ IDNO:156), a homolog of CBH2 of T. reesei. FIG. 90H depicts amino acidsequence of St6B (SEQ ID NO:157), a homolog of CBH2 of T. reesei. FIG.90I amino acid sequence of Tt6A (SEQ ID NO:158), a homolog of CBH2 of T.reesei.

DETAILED DESCRIPTION OF THE INVENTION

Unless defined otherwise, all technical and scientific terms used hereinhave the meaning as commonly understood by a skilled person in the artto which this invention belongs. Singleton, et al., DICTIONARY OFMICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, NewYork (1994), and Hale & Marham, THE HARPER COLLINS DICTIONARY OFBIOLOGY, Harper Perennial, N.Y. (1991) provide one of skill with ageneral dictionary of many of the terms used in this invention. Althoughany methods and materials similar or equivalent to those describedherein can be used in the practice of the present invention, thepreferred methods and materials are described. Numeric ranges areinclusive of the numbers defining the range. The invention is notlimited to the particular methodology, protocols, and reagentsdescribed, as these may vary.

The headings provided herein do not limit the various aspects orembodiments of the invention that can be had by reference to thespecification as a whole. Accordingly the terms defined below are morefully defined by reference to the specification as a whole.

The present disclosure provides compositions comprising a polypeptidehaving glycosyl hydrolase family 61 (“GH61”)/endoglucanase activity,polypeptides having GH61/endoglucanase activity, nucleotides encoding apolypeptide provided herein, vectors containing nucleotide providedherein, and cells containing nucleotide and/or vector provided herein.The present disclosure further provides methods of hydrolyzing a biomassmaterial and methods of reducing the viscosity of a biomass-containingmixture using a composition provided herein.

The term “isolated” as used herein with respect to nucleic acids, suchas DNA or RNA, refers to molecules separated from other DNAs or RNAs,respectively, which are present in the natural source of the nucleicacid. Moreover, by an “isolated nucleic acid” is meant to includenucleic acid fragments, which are not naturally occurring as fragmentsand would not be found in the natural state. The term “isolated” is alsoused herein to refer to polypeptides, which are isolated from othercellular proteins and is meant to encompass both purified andrecombinant polypeptides. The term “isolated” as used herein also refersto a nucleic acid or polypeptide that may be substantially free ofcellular material, viral material, or culture medium when produced byrecombinant DNA techniques. The term “isolated” as used hereinadditionally refers to a nucleic acid or polypeptide that may besubstantially free of chemical precursors or other chemicals whenchemically synthesized.

As used herein, a “variant” of polypeptide X refers to a polypeptidehaving the amino acid sequence of polypeptide X with one or more alteredamino acid residues. The variant may have conservative ornonconservative changes. Guidance in determining which amino acidresidues may be substituted, inserted, or deleted without affectingbiological activity may be found using computer programs known in theart, e.g., LASERGENE software (DNASTAR). A variant of the inventionincludes polypeptides comprising altered amino acid sequences incomparison with a precursor enzyme amino acid sequence, wherein thevariant enzyme retains the characteristic cellulolytic nature of theprecursor enzyme but may have altered properties in some specificaspects, e.g., an increased or decreased pH optimum, an increased ordecreased oxidative stability; an increased or decreasedthermostability, and increased or decreased level of specific activitytowards one or more substrates, as compared to the precursor enzyme.

As used herein, a polypeptide or nucleic acid that is “heterologous” toa host cell refers to a polypeptide or nucleic acid that does notnaturally occur in a host cell.

Reference to “about” a value or parameter herein includes (anddescribes) variations that are directed to that value or parameter perse. For example, description referring to “about X” includes descriptionof “X”.

As used herein and in the appended claims, the singular forms “a,” “or,”and “the” include plural referents unless the context clearly dictatesotherwise.

It is understood that aspects and variations of the methods andcompositions described herein include “consisting” and/or “consistingessentially of” aspects and variations.

Polypeptides

The disclosure provides polypeptides (e.g., isolated, synthetic, orrecombinant polypeptides) having GH61/endoglucanase activity. Forexample, the present disclosure provides GH61 endoglucanases fromvarious species or variants thereof, endoglucanase IV (or endoglucanase4) polypeptides (also described herein as “Eg4” or “EG4”, which are usedinterchangeably herein) from various species or variants thereof, andTrichoderma reesei Eg4 polypeptide or variants thereof. In some aspects,the polypeptide is isolated.

Glycoside Hydrolase Family 61 (“GH61”) Enzymes

Glycoside hydrolase family 61 (“GH61”) enzymes have been identified inEukaryota. A weak endoglucanase activity has been observed for Ce161Afrom Hypocrea jecorina (Karlsson et al, Eur J Biochem, 2001,268(24):6498-6507), which is thus said to have GH61/endoglucanaseactivity. GH61 polypeptides potentiate enzymatic hydrolysis oflignocellulosic substrates by cellulases (Harris et al, 2010,Biochemistry, 49(15) 3305-16). Studies on homologous polypeptidesinvolved in chitin degradation predict that GH61 polypeptides may employan oxidative hydrolysis mechanism that requires an electron donorsubstrate and in which divalent metal ions are involved (Vaaje-Kolstad,2010, Science, 330(6001), 219-22). This agrees with the observation thatthe synergistic effect of GH61 polypeptides on lignocellulosic substratedegradation is dependent on divalent ions (Harris et al, 2010,Biochemistry, 49(15) 3305-16). A number of available structures of GH61polypeptides have divalent atoms bound by a number of conserved aminoacid residues (Karkehabadi, 2008, J. Mol. Biol., 383(1) 144-54; Harriset al, 2010, Biochemistry, 49(15) 3305-16). It has been reported thatthe GH61 polypeptides have a flat surface at the metal binding site thatis formed by conserved residues and might be involved in substratebinding (Karkehabadi, 2008, J. Mol. Biol., 383(1), 144-54).

The present disclosure provides polypeptides having GH61/endoglucanaseactivity (e.g., isolated polypeptide) which can be a GH61 endoglucanaseor endoglucanase IV (“EG IV”) from various species, or can also be apolypeptide from various species corresponding to (sharing homologywith, sharing functional domains, sharing GH61 motif(s), and/or sharingconservative residues with) a GH61 endoglucanase (e.g., a Trichodermareesei Eg4 polypeptide). Such species include Trichoderma, Humicola,Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya,Podospora, Endothia, Mucor, Cochliobolus, Pyricularia, Chrysosporium,Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus,Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger,Aspergillus oryzae, Chrysosporium lucknowense, Fusarium bactridioides,Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusariumvenenatum, Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsisaneirina, Ceriporiopsis caregiea, Ceriporiopsis gilvescens,Ceriporiopsis pannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa,Ceriporiopsis subvermispora, Coprinus cinereus, Coriolus hirsutus,Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthorathermophila, Neurospora crassa, Neurospora intermedia, Penicilliumpurpurogenum, Penicillium canescens, Penicillium solitum, Penicilliumfuniculosum Phanerochaete chrysosporium, Phlebia radiate, Pleurotuseryngii, Talaromyces flavus, Thielavia terrestris, Trametes villosa,Trametes versicolor, Trichoderma harzianum, Trichoderma koningii,Trichoderma longibrachiatum, Trichoderma reesei, Trichoderma viride,Geosmithia emersonii, or G. stearothermophilus.

Polypeptides having GH61/endoglucanase activity include a number of GH61endoglucanases listed in FIG. 1. For example, suitable GH61endoglucanases include those comprising amino acid sequences that are atleast about 60% identical to the various sequences listed in FIG. 1,including, for example, those represented by their GenBank AccessionNumbers CAB97283.2, CAD70347.1, CAD21296.1, CAE81966.1, CAF05857.1,EAA26873.1, EAA29132.1, EAA30263.1, EAA33178.1, EAA33408.1, EAA34466.1,EAA36362.1, EAA29018.1, and EAA29347.1, or St61 from S. thermophilum24630, St61A from S. thermophilum 23839c, St61B from S. thermophilum46583, St61D from S. thermophilum 80312, Afu61a from A. fumigatusAfu3g03870 (NCBI Ref: XP_(—)748707), an endoglucanase having NCBI Ref:XP_(—)750843.1 from A. fumigatus Afu6g09540, an endoglucanase from A.fumigatus EDP47167, an endoglucanase from T. terrestris 16380, anendoglucanase from T. terrestris 155418, an endoglucanase from T.terrestris 68900, Cg61A (Accession Number EAQ86340.1) from C. globosum,T. reesei Eg7, T. reesei Eg4, and an endoglucanase with GenBankAccession Number XP_(—)752040 from A. fumigatus Af293. In some aspects,a suitable GH61 endoglucanase polypeptide of the invention comprises anamino acid sequence of at least about 60% (e.g., at least about 60%,65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%) sequence identity to any one of SEQ ID NOs: 1-29 and 148. In someaspects, a suitable GH61 endoglucanase polypeptide of the inventioncomprises one or more of the amino acid sequence motifs selected from:(1) SEQ ID NOs:84 and 88; (2) SEQ ID NOs:85 and 88; (3) SEQ ID NO:86;(4) SEQ ID NO:87; (5) SEQ ID NOs:84, 88 and 89; (6) SEQ ID NOs:85, 88,and 89; (7) SEQ ID NOs: 84, 88, and 90; (8) SEQ ID NOs: 85, 88 and 90;(9) SEQ ID NOs:84, 88 and 91; (10) SEQ ID NOs: 85, 88 and 91; (11) SEQID NOs: 84, 88, 89 and 91; (12) SEQ ID NOs: 84, 88, 90 and 91; (13) SEQID NOs: 85, 88, 89 and 91: and (14) SEQ ID NOs: 85, 88, 90 and 91. Thepolypeptide may be at least 100 (e.g., 110, 120, 130, 140, 150, 160,170, 180, 200, 220, 250 or more) residues in length.

Polypeptides having GH61/endoglucanase activity (e.g., isolatedpolypeptide) provided herein may also be a variant of a GH61endoglucanase, e.g., any of the polypeptides with amino acid sequencesshown FIG. 1 of the present disclosure. For example, suitable GH61endoglucanases include those represented by their GenBank AccessionNumbers CAB97283.2, CAD70347.1, CAD21296.1, CAE81966.1, CAF05857.1,EAA26873.1, EAA29132.1, EAA30263.1, EAA33178.1, EAA33408.1, EAA34466.1,EAA36362.1, EAA29018.1, and EAA29347.1, or St61 from S. thermophilum24630, St61A from S. thermophilum 23839c, St61B from S. thermophilum46583, St61D from S. thermophilum 80312, Afu61a from A. fumigatusAfu3g03870 (NCBI Ref: XP_(—)748707), an endoglucanase with NCBI Ref:XP_(—)750843.1 from A. fumigatus Afu6g09540, an endoglucanase from A.fumigatus EDP47167, an endoglucanase from T. terrestris 16380, anendoglucanase from T. terrestris 155418, an endoglucanase from T.terrestris 68900, Cg61A (EAQ86340.1) from C. globosum, T. reesei Eg7, T.reesei Eg4, and an endoglucanase with GenBank Accession: XP_(—)752040from A. fumigatus Af293. In some aspects, the polypeptide havingGH61/endoglucanase activity (e.g., isolated polypeptide) is a variant ofEG IV. In some aspects, the polypeptide having GH61/endoglucanaseactivity (e.g., isolated polypeptide) is a variant of a GH61endoglucanase, wherein the variant has an amino acid sequence having atleast about 60% (e.g., at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, or 99%) identity as any one of the amino acidsequences SEQ ID NOs: 1-29 and 148.

An alignment using amino acid sequences SEQ ID NOs:1-29 and 148 wasperformed and the alignment result is shown in FIG. 3. FIG. 2 shows thepercent identity and divergence results from comparison of the aminoacid sequences of the polypeptides. The alignment indicated that theGH61 endoglucanase polypeptides share certain sequence motifs, and suchmotifs are shown in FIG. 7 of the present disclosure.

Accordingly, the present disclosure provides polypeptides (e.g.,isolated, synthetic, or recombinant polypeptides) havingGH61/endoglucanase activity, which may be a GH61 endoglucanase or avariant thereof, and the variant may comprise at least one motif (atleast any of 2, 3, 4, 5, 6, 7, or 8) selected from SEQ ID NOs:84-91.Each of the “a”s in sequence motifs with SEQ ID NOs:84-91 (described inFIG. 7) represents an amino acid that may be any one of alanine,arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine,glycine, histidine, isoleucine, leucine, lysine, methionine,phenylalanine, proline, serine, threonine, tryptophan, tyrosine, orvaline. For example, in some aspects, the disclosure providespolypeptides (e.g., isolated, synthetic, or recombinant polypeptides)comprising at least one sequence motif, such as at least one (e.g., 2,3, 4, 5, 6, 7, or 8) of SEQ ID NOs: 84, 85, 86, 87, 88, 89, 90, and 91.In some aspects, the disclosure provides polypeptides (e.g., isolated,synthetic, or recombinant polypeptides) comprising one or more of thesequence motifs selected from the group consisting of: (1) SEQ ID NOs:84and 88; (2) SEQ ID NOs:85 and 88; (3) SEQ ID NO:86; (4) SEQ ID NO:87;(5) SEQ ID NOs:84, 88 and 89; (6) SEQ ID NOs:85, 88, and 89; (7) SEQ IDNOs: 84, 88, and 90; (8) SEQ ID NOs: 85, 88 and 90; (9) SEQ ID NOs:84,88 and 91; (10) SEQ ID NOs: 85, 88 and 91; (11) SEQ ID NOs: 84, 88, 89and 91; (12) SEQ ID NOs: 84, 88, 90 and 91; (13) SEQ ID NOs: 85, 88, 89and 91: and (14) SEQ ID NOs: 85, 88, 90 and 91, over a region of atleast about 10, e.g., at least about any of 15, 20, 25, 30, 35, 40, 45,50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225,250, 275, 300, 325, or 350 residues, or over the full length of theimmature polypeptide, the full length mature polypeptide, the fulllength of the conserved domain, and/or the full length CBM. Theconserved domain can be a predicted catalytic domain (“CD”). Exemplarypolypeptides also include fragments of at least about 10, e.g., at leastabout any of 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100,150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 residues in length.The fragments can comprise a conserved domain and/or a CBM. Where afragment comprises a conserved domain and a CBM of an enzyme, thefragment optionally includes a linker separating the two. The linker canbe a native linker or a heterologous linker In some aspects, thepolypeptide has GH61/endoglucanase activity.

In some aspects, the polypeptide having GH61/endoglucanase activity is aGH61 endoglucanase or a variant thereof, an enzyme comprising any one ofSEQ ID NOs: 1-29 and 148, or a variant thereof, an EG IV or a variantthereof, or a T. reesei Eg4 or a variant thereof. A variant describedhere has endoglucanase activity. The polypeptide havingGH61/endoglucanase activity (including a variant) may comprise a CBMdomain (e.g., functional CBM domain). The polypeptide havingGH61/endoglucanase activity (including a variant) may comprise acatalytic domain (e.g., function catalytic domain).

T. reesei Eg4 is a GH61 endoglucanase polypeptide. The amino acidsequence of T. reesei Eg4 (SEQ ID NO:27) is shown in FIGS. 1, 4B and 5.SEQ ID NO:27 is the sequence of the immature T. reesei Eg4. T. reeseiEg4 has a predicted signal sequence corresponding to residues 1 to 21 ofSEQ ID NO:27 (underlined); cleavage of the signal sequence is predictedto yield a mature polypeptide having a sequence corresponding toresidues 22 to 344 of SEQ ID NO:27. The predicted conserved domainscorrespond to residues 22-256 and 307-343 of SEQ ID NO:27, with thelatter being the predicted carbohydrate-binding domain (CBM). T. reeseiEg4 was shown to have endoglucanse activity in, for example, anenzymatic assay using carboxy methyl cellulose as substrates. Methods ofmeasuring endoglucanse activity are also known to one skilled in theart.

The disclosure further provides a variant of Trichoderma reesei Eg4polypeptide, which may comprise a sequence having at least about 60%(e.g., at least about 65%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%,79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, or 99%) sequence identity to at leastabout 50 (e.g., at least about 55, 60, 65, 70, 75, 100, 125, 150, 175,200, 250, or 300) contiguous amino acid residues among residues 22 to344 of SEQ ID NO:27. For example, the disclosure provides variants of T.reesei Eg4 polypeptide. Such variants may have at least about 70% (e.g.,at least about 70%, 75%, 80%, 85%, 88%, 90%, 92.5%, 95%, 96%, 97%, 98%,or 99%) identity to residues 22 to 344 of SEQ ID NO:27. The polypeptideor a variant thereof may be isolated. The polypeptide or a variantthereof may have endoglucanase activity.

T. reesei Eg4 residues H22, H107, H184, Q193, and Y195 were predicted tofunction as metal coordinator residues; residues D61 and G63 werepredicted to be conserved surface residues; and residue Y232 werepredicted to be involved in activity, based on an amino acid sequencealignment of a number of known endoglucanases, e.g., an endoglucanasefrom T. terrestris (Accession No. ACE10234, also termed “TtEG” herein)(SEQ ID NO:29), and another endoglucanse Eg7 (Accession No. ADA26043.1)from T. reesei (also termed “TrEGb” or “TrEG7” herein), with T. reeseiEg4 (see, FIG. 5). The predicted conserved residues in T. reesei Eg4 Aare shown in FIGS. 6A and 6B. A variant of T. reesei Eg4 polypeptide maybe unaltered, as compared to a native T. reesei Eg4, at residues H22,H107, H184, Q193, Y195, D61, G63, and Y232. A variant of T. reesei Eg4polypeptide may be unaltered in at least 60%, 70%, 80%, 90%, 95%, 98%,or 99% of the amino acid residues that are conserved among TrEGb, TtEG,and T. reesei Eg4, as shown in the alignment of FIG. 5. A variant of T.reesei Eg4 polypeptide may comprise the entire predicted conserveddomains of native T. reesei Eg4. See FIGS. 5 and 6. An exemplary variantof T. reesei Eg4 polypeptide comprises a sequence having at least aboutany of 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identity to the mature T. reesei Eg4sequence shown in FIG. 4B (e.g., residues 22 to 344 of SEQ ID NO:27). Insome aspects, the variant of T. reesei Eg4 polypeptide has endoglucanse(e.g., endoglucanse IV (EGIV)) activity.

In some aspects, a variant of T. reesei Eg4 polypeptide hasendoglucanase activity and comprises an amino acid sequence with atleast about any of 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequenceidentity to the amino acid sequence of SEQ ID NO:27, or to residues (i)22-255, (ii) 22-343, (iii) 307-343, (iv) 307-344, or (v) 22-344 of SEQID NO:27.

In some aspects, the polypeptide or a variant thereof comprises residuescorresponding to at least about 3 residues (e.g., at least about any of4, 5, 6, 7, 8, 9, 10, 11, or 12) of H22, D61, G63, C77, H107, R177,E179, H184, Q193, C198, Y195, and Y232 of SEQ ID NO:27. In some aspects,the polypeptide or a variant thereof comprises residues corresponding toH22, D61, G63, C77, H107, R177, E179, H184, Q193, C198, Y195, and Y232of SEQ ID NO:27. In some aspects, the polypeptide or a variant thereofcomprises residues corresponding to at least 3 residues (e.g., at leastabout any of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or19) of G313, Q314, C315, G316, G317, S321, G322, P323, T324, C326, A327,T331, C332, N336, Y338, Y339, Q341, C342, and L343 of SEQ ID

NO:27. In some aspects, the polypeptide or a variant thereof comprisesresidues corresponding to G313, Q314, C315, G316, G317, S321, G322,P323, T324, C326, A327, T331, C332, N336, Y338, Y339, Q341, C342, andL343 of SEQ ID NO:27. In some aspects, the polypeptide or a variantthereof comprises a CBM domain (e.g., functional CBM domain). In someaspects, the polypeptide or a variant thereof comprises a catalyticdomain (e.g., functional catalytic domain). The polypeptide suitably hasendoglucanase activity.

A variant of GH61 endoglucanase, an endoglucanase comprising any one ofSEQ ID NOs:1-29 and 148, an EG IV, or Trichoderma reesei Eg4 polypeptidemay be made using amino acid substitution. Conservative substitutionsare shown in the table below under the heading of “conservativesubstitutions”. Substitutions may also be exemplary substitution shownin the table below.

TABLE 1 Amino Acid Substitutions. Conservative Original ResidueSubstitutions Exemplary Substitutions Ala (A) Val Val; Leu; Ile Arg (R)Lys Lys; Gln; Asn Asn (N) Gln Gln; His; Asp, Lys; Arg Asp (D) Glu Glu;Asn Cys (C) Ser Ser; Ala Gln (Q) Asn Asn; Glu Glu (E) Asp Asp; Gln Gly(G) Ala Ala His (H) Arg Asn; Gln; Lys; Arg Ile (I) Leu Leu; Val; Met;Ala; Phe; Norleucine Leu (L) Ile Norleucine; Ile; Val; Met; Ala; Phe Lys(K) Arg Arg; Gln; Asn Met (M) Leu Leu; Phe; Ile Phe (F) Tyr Leu; Val;Ile; Ala; Tyr Pro (P) Ala Ala Ser (S) Thr Thr Thr (T) Ser Ser Trp (W)Tyr Tyr; Phe Tyr (Y) Phe Trp; Phe; Thr; Ser Val (V) Leu Ile; Leu; Met;Phe; Ala; Norleucine

Substantial modifications in the enzymatic properties of the polypeptideare accomplished by selecting substitutions that differ significantly intheir effect on maintaining (a) the structure of the polypeptidebackbone in the area of the substitution, for example, as a sheet orhelical conformation, (b) the charge or hydrophobicity of the moleculeat the target site, or (c) the bulk of the side chain. Naturallyoccurring residues are divided into groups based on common side-chainproperties:

(1) Non-polar: Norleucine, Met, Ala, Val, Leu, Ile;

(2) Polar without charge: Cys, Ser, Thr, Asn, Gln;

(3) Acidic (negatively charged): Asp, Glu;

(4) Basic (positively charged): Lys, Arg;

(5) Residues that influence chain orientation: Gly, Pro; and

(6) Aromatic: Trp, Tyr, Phe, His.

Non-conservative substitutions are made by exchanging a member of one ofthese classes for another class. Any cysteine residue not involved inmaintaining the proper conformation of the polypeptide also may besubstituted, generally with serine, to improve the oxidative stabilityof the molecule and prevent aberrant cross-linking. Conversely, cysteinebond(s) may be added to the polypeptide to improve its stability.

In some aspects, a polypeptide (e.g., isolated, synthetic, orrecombinant polypeptide) having GH61/endoglucanase activity is a fusionor chimeric polypeptide that includes a domain of a polypeptide of thepresent disclosure attached to one or more fusion segments, which aretypically heterologous to the polypeptide (e.g., derived from adifferent source than the polypeptide of the disclosure). Suitablefusion or chimeric segments include, without limitation, segments thatcan enhance a polypeptide's stability, provide other desirablebiological activity or enhanced levels of desirable biological activity,and/or facilitate purification of the polypeptide (e.g., by affinitychromatography). A suitable fusion segment can be a domain of any sizethat has the desired function (e.g., imparts increased stability,solubility, action or biological activity; and/or simplifiespurification of a polypeptide). A fusion or hybrid polypeptide of theinvention can be constructed from two or more fusion or chimericsegments, each of which or at least two of which are derived from adifferent source or microorganism. Fusion or hybrid segments can bejoined to amino and/or carboxyl termini of the domain(s) of apolypeptide of the present disclosure. The fusion segments can besusceptible to cleavage. There may be some advantage in having thissusceptibility, for example, it may enable straight-forward recovery ofthe polypeptide of interest. Fusion polypeptides may be produced byculturing a recombinant cell transfected with a fusion nucleic acid thatencodes a polypeptide, which includes a fusion segment attached toeither the carboxyl or amino terminal end, or fusion segments attachedto both the carboxyl and amino terminal ends, of a polypeptide, or adomain thereof.

Accordingly, polypeptides of the present disclosure also includeexpression products of gene fusions (e.g., an overexpressed, soluble,and active form of expression product), of mutagenized genes (e.g.,genes having codon modifications to enhance gene transcription andtranslation), and of truncated genes (e.g., genes having signalsequences removed or substituted with a heterologous signal sequence).

Glycosyl hydrolases that utilize insoluble substrates are often modularenzymes. They may comprise catalytic modules appended to one or morenon-catalytic carbohydrate-binding domains (CBMs). In nature, CBMs arethought to promote the glycosyl hydrolase's interaction with its targetsubstrate polysaccharide. Thus, the disclosure provides chimeric enzymeshaving altered substrate specificity; including, for example, chimericenzymes having multiple substrates as a result of “spliced-in”heterologous CBMs. The heterologous CBMs of the chimeric enzymes of thedisclosure can also be designed to be modular, such that they areappended to a catalytic module or catalytic domain (a “CD”, e.g., at anactive site), which can likewise be heterologous or homologous to theglycosyl hydrolase.

Thus, the disclosure provides peptides and polypeptides consisting of,or comprising, CBM/CD modules, which can be homologously paired orjoined to form chimeric (heterologous) CBM/CD pairs. Thus, thesechimeric polypeptides/peptides can be used to improve or alter theperformance of an enzyme of interest.

In some aspects, there is provided a polypeptide havingGH61/endoglucanase activity, which comprises at least one CD and/or CBMof any one of the polypeptides with sequences shown in FIG. 1 of thepresent disclosure. For example, suitable GH61 endoglucanasepolypeptides of FIG. 1 includes those that are represented by theirGenBank Accession Numbers CAB97283.2, CAD70347.1, CAD21296.1,CAE81966.1, CAF05857.1, EAA26873.1, EAA29132.1, EAA30263.1, EAA33178.1,EAA33408.1, EAA34466.1, EAA36362.1, EAA29018.1, and EAA29347.1, or St61from S. thermophilum 24630, St61A from S. thermophilum 23839c, St61Bfrom S. thermophilum 46583, St61D from S. thermophilum 80312, Afu61afrom A. fumigatus Afu3g03870 (NCBI Ref: XP_(—)748707), an endoglucanaseof NCBI Ref: XP_(—)750843.1 from A. fumigatus Afu6g09540, anendoglucanase of A. fumigatus EDP47167, an endoglucanase of T.terrestris 16380, an endoglucanase of T. terrestris 155418, anendoglucanase of T. terrestris 68900, Cg61A (EAQ86340.1) from C.globosum, T. reesei Eg7, T. reesei Eg4, and an endoglucanase withGenBank Accession: XP_(—)752040 from A. fumigatus Af293. The polypeptidemay suitably be a fusion polypeptide comprising functional domains fromtwo or more different polypeptides (e.g., a CBM from one polypeptidelinked to a CD from another polypeptide).

The polypeptides of the disclosure can suitably be obtained and/or usedin “substantially pure” form. For example, a polypeptide of thedisclosure constitutes at least about 80 wt. % (e.g., at least about anyof 85 wt. %, 90 wt. %, 91 wt. %, 92 wt. %, 93 wt. %, 94 wt. %, 95 wt. %,96 wt. %, 97 wt. %, 98 wt. %, or 99 wt. %) of the total protein in agiven composition, which also includes other ingredients such as abuffer or solution.

Also the polypeptides of the disclosure may suitably be obtained and/orused in culture broths (e.g., a filamentous fungal culture broth). Theculture broth may be an engineered enzyme composition, e.g., the culturebroth may be produced by a recombinant host cell engineered to express aheterologous polypeptide of the disclosure, or by a recombinant hostcell engineered to express an endogenous polypeptide of the disclosurein greater or lesser amounts than the endogenous expression levels(e.g., in an amount that is 1-, 2-, 3-, 4-, 5-, or more-fold greater orless than the endogenous expression levels). Furthermore, the culturebroths may be produced by certain “integrated” host cell strains thatare engineered to express a plurality of the polypeptides of thedisclosure in desired ratios.

Nucleic Acids, Expression Cassettes, Vectors, and Host Cells

The disclosure provides nucleic acids (e.g., isolated, synthetic orrecombinant nucleic acids) encoding polypeptides provided above, e.g.,polypeptides having GH61/endoglucanase activity, GH61 endoglucanase or avariant thereof, EG IV or a variant thereof, T. reesei Eg4 or a variantthereof. In certain aspects, the disclosure provides nucleic acids(e.g., isolated, synthetic or recombinant nucleic acids) encoding apolypeptide comprising any one of SEQ ID NOs:1-29 and 148, or apolypeptide having at least about 60%, 65%, 70%, 75%, 80%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%identity to any one of SEQ ID NOs: 1-29 and 148.

In certain aspects, the disclosure provides nucleic acids (e.g.,isolated, synthetic or recombinant nucleic acids) encoding any one ofthe polypeptides having GH61/endoglucanase activity (including a variantof a GH61 endoglucanase) comprising one or more sequence motif selectedfrom: (1) SEQ ID NOs:84 and 88; (2) SEQ ID NOs:85 and 88; (3) SEQ IDNO:86; (4) SEQ ID NO:87; (5) SEQ ID NOs:84, 88 and 89; (6) SEQ IDNOs:85, 88, and 89; (7) SEQ ID NOs: 84, 88, and 90; (8) SEQ ID NOs: 85,88 and 90; (9) SEQ ID NOs:84, 88 and 91; (10) SEQ ID NOs: 85, 88 and 91;(11) SEQ ID NOs: 84, 88, 89 and 91; (12) SEQ ID NOs: 84, 88, 90 and 91;(13) SEQ ID NOs: 85, 88, 89 and 91: and (14) SEQ ID NOs: 85, 88, 90 and91. The disclosure further provides nucleic acids (e.g., isolated,synthetic or recombinant nucleic acids) encoding a polypeptide havingGH61/endoglucanase activity (including a variant of a GH61endoglucanase) that comprises a CBM domain (e.g., functional CBM domain)and/or catalytic domain (e.g., functional catalytic domain).

The disclosure further provides nucleic acids (e.g., isolated, syntheticor recombinant nucleic acids) encoding variants of T. reesei Eg4polypeptide. Such variants may have at least about 60% (e.g., at leastabout any of 60%, 65%, 70%, 75%, 80%, 85%, 88%, 90%, 92.5%, 95%, 96%,97%, 98%, or 99%) sequence identity to residues 22 to 344 of SEQ IDNO:27. In some aspects, the polypeptide or a variant thereof hasendoglucanase activity. The polypeptide or a variant thereof maycomprise residues corresponding to at least about 5 residues (e.g., atleast about any of 6, 7, 8, 9, 10, 11, or 12) of H22, D61, G63, C77,H107, R177, E179, H184, Q193, C198, Y195, and Y232 of SEQ ID NO:27. Thepolypeptide or a variant thereof may comprise residues corresponding toH22, D61, G63, C77, H107, R177, E179, H184, Q193, C198, Y195, and Y232of SEQ ID NO:27. The polypeptide or a variant thereof may compriseresidues corresponding to at least 5 residues (e.g., at least about anyof 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19) of G313, Q314,C315, G316, G317, S321, G322, P323, T324, C326, A327, T331, C332, N336,Y338, Y339, Q341, C342, and L343 of SEQ ID NO:27. In some aspects, thepolypeptide or a variant thereof comprises residues corresponding toG313, Q314, C315, G316, G317, S321, G322, P323, T324, C326, A327, T331,C332, N336, Y338, Y339, Q341, C342, and L343 of SEQ ID NO:27.

The disclosure provides nucleic acids (e.g., isolated, synthetic orrecombinant nucleic acids) comprising a nucleic acid sequence having atleast about 70%, e.g., at least about any of 71%, 72%, 73%, 74%, 75%,76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%; 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or complete (100%)identity to nucleic acid sequence SEQ ID NO:30, over a region of atleast about 10, e.g., at least about any of 15, 20, 25, 30, 35, 40, 45,50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700,750, 800, 850, 900, 950, 1000, or 1050 nucleotides. In some aspects, thedisclosure provides nucleic acids encoding any one of the polypeptidesprovided herein. Also provided herein are isolated nucleic acids havingat least about 80% (e.g., at least about any of 85%, 88%, 90%, 92.5%,95%, 96%, 97%, 98%, or 99%) identity to SEQ ID NO:30.

In some aspects, there is provided a nucleic acid (e.g., isolated,synthetic or recombinant nucleic acid) encoding a polypeptide comprisingan amino acid sequence with at least 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acidsequence of SEQ ID NO:27, or to residues (i) 22-255, (ii) 22-343, (iii)307-343, (iv) 307-344, or (v) 22-344 of SEQ ID NO:27. In some aspects,there is provided a nucleic acid (e.g., isolated, synthetic orrecombinant nucleic acid) having at least 70% (e.g., at least 70%, 75%,80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more)sequence identity to SEQ ID NO:30, or a nucleic acid that is capable ofhybridizing under high stringency conditions to a complement of SEQ IDNO:30, or to a fragment thereof. As used herein, the term “hybridizesunder low stringency, medium stringency, high stringency, or very highstringency conditions” describes conditions for hybridization andwashing. Guidance for performing hybridization reactions can be found inCurrent Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989),6.3.1-6.3.6. Aqueous and nonaqueous methods are described in thatreference and either method can be used. Specific hybridizationconditions referred to herein are as follows: 1) low stringencyhybridization conditions in 6× sodium chloride/sodium citrate (SSC) atabout 45° C., followed by two washes in 0.2×SSC, 0.1% SDS at least at50° C. (the temperature of the washes can be increased to 55° C. for lowstringency conditions); 2) medium stringency hybridization conditions in6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1%SDS at 60° C.; 3) high stringency hybridization conditions in 6×SSC atabout 45° C., followed by one or more washes in 0.2.×SSC, 0.1% SDS at65° C.; and preferably 4) very high stringency hybridization conditionsare 0.5M sodium phosphate, 7% SDS at 65° C., followed by one or morewashes at 0.2×SSC, 1% SDS at 65° C. Very high stringency conditions (4)are the preferred conditions unless otherwise specified.

The disclosure also provides expression cassettes and/or vectorscomprising any of the above-described nucleic acids. The nucleic acidencoding a polypeptide such as an enzyme of the disclosure may beoperably linked to a promoter. Specifically where recombinant expressionin a filamentous fungal host is desired, the promoter can be afilamentous fungal promoter. The nucleic acids can be, e.g., under thecontrol of heterologous promoters. The nucleic acids can also beexpressed under the control of constitutive or inducible promoters.Examples of promoters that can be used include, but are not limited to,a cellulase promoter, a xylanase promoter, the 1818 promoter (previouslyidentified as a highly expressed protein by EST mapping Trichoderma).For example, the promoter can suitably be a cellobiohydrolase,endoglucanase, or β-glucosidase promoter. A particularly suitablepromoter can be, for example, a T. reesei cellobiohydrolase,endoglucanase, or β-glucosidase promoter. For example, the promoter is acellobiohydrolase I (cbh1) promoter. Non-limiting examples of promotersinclude a cbh1, cbh2, egl1, egl2, egl3, egl4, egl5, pki1, gpd1, xyn1, orxyn2 promoter. Additional non-limiting examples of promoters include aT. reesei cbh1, cbh2, egl1, egl2, egl3, egl4, egl5, pki1, gpd1, xyn1, orxyn2 promoter.

As used herein, the term “operably linked” means that selectednucleotide sequence (e.g., encoding a polypeptide described herein) isin proximity with a promoter to allow the promoter to regulateexpression of the selected DNA. In addition, the promoter is locatedupstream of the selected nucleotide sequence in terms of the directionof transcription and translation. By “operably linked” is meant that anucleotide sequence and a regulatory sequence(s) are connected in such away as to permit gene expression when the appropriate molecules (e.g.,transcriptional activator proteins) are bound to the regulatorysequence(s).

The present disclosure further provides host cells containing any of thepolynucleotides vectors, or expression cassettes described herein. Thepresent disclosure also provides host cells that can be used to expressone or more polypeptides of the disclosure.

Suitable host cells include cells of any microorganism (e.g., cells of abacterium, a protist, an alga, a fungus (e.g., a yeast or filamentousfungus), or other microbe), and are preferably cells of a bacterium, ayeast, or a filamentous fungus.

Suitable host cells of the bacterial genera include, but are not limitedto, cells of Escherichia, Bacillus, Lactobacillus, Pseudomonas, andStreptomyces. Suitable cells of bacterial species include, e.g., cellsof Escherichia coli, Bacillus subtilis, Bacillus licheniformis,Lactobacillus brevis, Pseudomonas aeruginosa, or Streptomyces lividans.

Suitable host cells of the genera of yeast include, but are not limitedto, cells of Saccharomyces, Schizosaccharomyces, Candida, Hansenula,Pichia, Kluyveromyces, and Phaffia. Suitable cells of yeast speciesinclude, but are not limited to, cells of Saccharomyces cerevisiae,Schizosaccharomyces pombe, Candida albicans, Hansenula polymorpha,Pichia pastoris, P. canadensis, Kluyveromyces marxianus, and Phaffiarhodozyma.

Suitable host cells of filamentous fungi include all filamentous formsof the subdivision Eumycotina. Suitable cells of filamentous fungalgenera include, but are not limited to, cells of Acremonium,Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysoporium,Coprinus, Coriolus, Corynascus, Chaertomium, Cryptococcus, Filobasidium,Fusarium, Gibberella, Humicola, Magnaporthe, Mucor, Myceliophthora,Mucor, Neocallimastix, Neurospora, Paecilomyces, Penicillium,Phanerochaete, Phlebia, Piromyces, Pleurotus, Scytaldium, Schizophyllum,Sporotrichum, Talaromyces, Thermoascus, Thielavia, Tolypocladium,Trametes, and Trichoderma. Suitable cells of filamentous fungal speciesinclude, but are not limited to, cells of Aspergillus awamori,Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus,Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae,Chrysosporium lucknowense, Fusarium bactridioides, Fusarium cerealis,Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum,Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusariumoxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum,Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum,Fusarium torulosum, Fusarium trichothecioides, Fusarium venenatum,Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsis aneirina,Ceriporiopsis caregiea, Ceriporiopsis gilvescens, Ceriporiopsispannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa, Ceriporiopsissubvermispora, Coprinus cinereus, Coriolus hirsutus, Humicola insolens,Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila,Neurospora crassa, Neurospora intermedia, Penicillium purpurogenum,Penicillium canescens, Penicillium solitum, Penicillium funiculosumPhanerochaete chrysosporium, Phlebia radiate, Pleurotus eryngii,Talaromyces flavus, Thielavia terrestris, Trametes villosa, Trametesversicolor, Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, Trichoderma reesei, and Trichoderma viride.

The disclosure provides a host cell, e.g., a recombinant fungal hostcell or a recombinant filamentous fungus, engineered to recombinantlyexpress a polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof).

The present disclosure also provides a recombinant host cell e.g., arecombinant fungal host cell or a recombinant microorganism, e.g., afilamentous fungus, such as a recombinant T. reesei, that is engineeredto recombinantly express T. reesei Xyn3, T. reesei Bgl1 (also termed“Tr3A”), Fv3A, Fv43D, and Fv51A polypeptides. For example, therecombinant host cell is suitably a T. reesei host cell. The recombinantfungus is suitably a recombinant T. reesei. The disclosure provides, forexample, a T. reesei host cell engineered to recombinantly express T.reesei Eg4, T. reesei Xyn3, T. reesei Bgl1, Fv3A, Fv43D, and Fv51Apolypeptides. Alternatively the present disclosure also provides arecombinant host cell or a recombinant microorganism that is, e.g., anAspergillus (such as an A. oryzae, A. niger) host cell or a recombinantAspergillus engineered to recombinantly express the polypeptidesdescribed herein.

Additionally the disclosure provides a recombinant host cell orrecombinant organism that is engineered to express an enzyme blendcomprising suitable enzymes in ratios suitable for saccharification. Therecombinant host cell is, for example, a fungal host cell or a bacterialhost cell. The recombinant fungus is, e.g., a recombinant T. reesei, A.oryzae, A. niger, or yeast. The recombinant fungal host cell may be,e.g., a T. reesei, A. oryzae, A. niger, or yeast cell. The recombinantbacterial host cell may be, e.g., a Bascillus subtilis, or an E. colicell. The recombinant bacterial organism may be, e.g., a Bascillussubtilis or an E. coli. Examples of enzyme ratios/amounts present insuitable enzyme blends are described herein such as below.

Compositions

The disclosure also provides compositions (e.g., non-naturally occurringcompositions) such as enzyme compositions containing cellulase(s) and/orhemicellulase(s), which can be used to hydrolyze biomass material and/orreduce the viscosity of biomass mixture (e.g., biomass saccharificationmixture containing enzyme and substrate).

Cellulases include enzymes capable of hydrolyzing cellulose(beta-1,4-glucan or beta D-glucosidic linkages) polymers to glucose,cellobiose, cellooligosaccharides, and the like. Cellulases have beentraditionally divided into three major classes: endoglucanases (EC3.2.1.4) (“EG”), exoglucanases or cellobiohydrolases (EC 3.2.1.91)(“CBH”) and β-glucosidases (β-D-glucoside glucohydrolase; EC 3.2.1.21)(“BG”) (Knowles et al., 1987, Trends in Biotechnology 5(9):255-261;Shulein, 1988, Methods in Enzymology, 160:234-242). Endoglucanases actmainly on the amorphous parts of the cellulose fiber, whereascellobiohydrolases are also able to degrade crystalline cellulose.Hemicellulases include, for example, xylanases, β-xylosidases, andL-α-arabinofuranosidases.

The composition of the invention may be a multi-enzyme blend, comprisingmore than one enzyme. The enzyme composition of the invention cansuitably include one or more additional enzymes derived from othermicroorganisms, plants, or organisms. Synergistic enzyme combinationsand related methods are contemplated. The disclosure includes methodsfor identifying the optimum ratios of the enzymes included in the enzymecompositions for degrading various types of biomass materials. Thesemethods include, e.g., tests to identify the optimum proportion orrelative weights of enzymes to be included in the enzyme composition ofthe invention in order to effectuate efficient conversion of varioussubstrates (e.g., lignocellulosic substrates) to their constituentfermentable sugars.

The cell walls of higher plants are comprised of a variety ofcarbohydrate polymer (CP) components. These CP interact through covalentand non-covalent means, providing the structural integrity required toform rigid cell walls and resist turgor pressure in plants. The major CPfound in plants is cellulose, which forms the structural backbone of thecell wall. During cellulose biosynthesis, chains of poly-β-1,4-D-glucoseself associate through hydrogen bonding and hydrophobic interactions toform cellulose microfibrils, which further self-associate to form largerfibrils. Cellulose microfibrils are often irregular structurally andcontain regions of varying crystallinity. The degree of crystallinity ofcellulose fibrils depends on how tightly ordered the hydrogen bonding isbetween and among its component cellulose chains. Areas withless-ordered bonding, and therefore more accessible glucose chains, arereferred to as amorphous regions. The general model for cellulosedepolymerization to glucose involves a minimum of three distinctenzymatic activities. Endoglucanases cleave cellulose chains internallyto shorter chains in a process that increases the number of accessibleends, which are more susceptible to exoglucanase activity than theintact cellulose chains. These exoglucanases (e.g., cellobiohydrolases)are specific for either reducing ends or non-reducing ends, liberating,in most cases, cellobiose, the dimer of glucose. The accumulatingcellobiose is then subject to cleavage by cellobiases (e.g.,β-1,4-glucosidases) to glucose. Cellulose contains only anhydro-glucose.In contrast, hemicellulose contains a number of different sugarmonomers. For instance, aside from glucose, sugar monomers inhemicellulose can also include xylose, mannose, galactose, rhamnose, andarabinose. Hemicelluloses mostly contain D-pentose sugars andoccasionally small amounts of L-sugars. Xylose is typically present inthe largest amount, but mannuronic acid and galacturonic acid also tendto be present. Hemicelluloses include xylan, glucuronoxylan,arabinoxylan, glucomannan, and xyloglucan.

The compositions (e.g., enzymes and multi-enzyme compositions) of thedisclosure can be used for saccharification of cellulose materials(e.g., glucan) and/or hemicellulose materials (e.g., xylan,arabinoxylan, and xylan- or arabinoxylan-containing substrates). Theenzyme blend/composition is suitably a non-naturally occurringcomposition.

The enzyme compositions provided herein may comprise a mixture ofxylan-hydrolyzing, hemicellulose- and/or cellulose-hydrolyzing enzymes,which include at least one, several, or all of a cellulase, including aglucanase; a cellobiohydrolase; an L-α-arabinofuranosidase; a xylanase;a β-glucosidase; and a β-xylosidase. The present disclosure alsoprovides enzyme compositions that may be non-naturally occurringcompositions. As used herein, the term “enzyme compositions” refers to:(1) a composition made by combining component enzymes, whether in theform of a fermentation broth or partially or completely isolated orpurified; (2) a composition produced by an organism modified to expressone or more component enzymes; in certain embodiments, the organism usedto express one or more component enzymes can be modified to delete oneor more genes; in certain other embodiments, the organism used toexpress one or more component enzymes can further comprise proteinsaffecting xylan hydrolysis, hemicellulose hydrolysis, and/or cellulosehydrolysis; (3) a composition made by combining component enzymessimultaneously, separately, or sequentially during a saccharification orfermentation reaction; (4) an enzyme mixture produced in situ, e.g.,during a saccharification or fermentation reaction; (5) a compositionproduced in accordance with any or all of the above (1)-(4).

The term “fermentation broth” as used herein refers to an enzymepreparation produced by fermentation that undergoes no or minimalrecovery and/or purification subsequent to fermentation. For example,microbial cultures are grown to saturation, incubated undercarbon-limiting conditions to allow protein synthesis (e.g., expressionof enzymes). Then, once the enzyme(s) are secreted into the cell culturemedia, the fermentation broths can be used. The fermentation broths ofthe disclosure can contain unfractionated or fractionated contents ofthe fermentation materials derived at the end of the fermentation. Forexample, the fermentation broths of the invention are unfractionated andcomprise the spent culture medium and cell debris present after themicrobial cells (e.g., filamentous fungal cells) undergo a fermentationprocess. The fermentation broth can suitably contain the spent cellculture media, extracellular enzymes, and live or killed microbialcells. Alternatively, the fermentation broths can be fractionated toremove the microbial cells. In those cases, the fermentation broths can,for example, comprise the spent cell culture media and the extracellularenzymes.

The enzyme compositions such as cellulase compositions provided hereinmay be capable of achieving at least 0.1 (e.g. 0.1 to 0.4) fractionproduct as determined by the calcofluor assay. All chemicals used wereof analytical grade. Avicel PH-101 was purchased from FMC BioPolymer(Philadelphia, Pa.). Cellobiose and calcofluor white were purchased fromSigma (St. Louise, Mo.). Phosphoric acid swollen cellulose (PASC) wasprepared from Avicel PH-101 using an adapted protocol of Walseth, TAPPI1971, 35:228 and Wood, Biochem. J. 1971, 121:353-362. In short, Avicelwas solubilized in concentrated phosphoric acid then precipitated usingcold deionized water. After the cellulose is collected and washed withmore water to neutralize the pH, it was diluted to 1% solids in 50 mMsodium acetate pH5. All enzyme dilutions were made into 50 mM sodiumacetate buffer, pH5.0. GC220 Cellulase (Danisco US Inc., Genencor) wasdiluted to 2.5, 5, 10, and 15 mg protein/G PASC, to produce a linearcalibration curve. Samples to be tested were diluted to fall within therange of the calibration curve, i.e. to obtain a response of 0.1 to 0.4fraction product. 150 μL of cold 1% PASC was added to 20 μL of enzymesolution in 96-well microtiter plates. The plate was covered andincubated for 2 h at 50° C., 200 rpm in an Innova incubator/shaker. Thereaction was quenched with 100 μL of 50 μg/mL Calcofluor in 100 mMGlycine, pH10. Fluorescence was read on a fluorescence microplate reader(SpectraMax M5 by Molecular Devices) at excitation wavelength Ex=365 nmand emission wavelength Em=435 nm. The result is expressed as thefraction product according to the equation:

FP=1−(Fl sample−Fl buffer w/cellobiose)/(Fl zero enzyme−Fl bufferw/cellobiose),

wherein FP is fraction product, and Fl=fluorescence units.

Any of the enzymes described specifically herein can be combined withany one or more of the enzymes described herein or with any otheravailable and suitable enzymes, to produce a suitable multi-enzymeblend/composition. The disclosure is not restricted or limited to thespecific exemplary combinations listed below.

Exemplary Compositions

There are provided non-naturally occurring compositions comprising apolypeptide having GH61/endoglucanase activity. The invention alsoprovides a non-naturally occurring composition comprising wholecellulase comprising a polypeptide having GH61/endoglucanase activity(e.g., whole cellulase enriched with a polypeptide havingGH61/endoglucanase activity such as endoglucanase IV (e.g., T. reeseiEg4 polypeptide-enriched whole cellulase)). The polypeptide havingGH61/endoglucanase activity may be any polypeptide havingGH61/endoglucanase activity provided herein. In some aspects, thepolypeptide having GH61/endoglucanase activity is T. reesei Eg4 or avariant thereof. A variant of T. reesei Eg4 can be any of the variantsprovided above.

Endoglucanase is referred to herein as “Eg” or “Egl,” interchangeably,in the present disclosure including figures.

As used herein, the term “naturally occurring composition” refers to acomposition produced by a naturally occurring source, comprising one ormore enzymatic components or activities, wherein each of the componentsor activities is found at the ratio and level produced by thenaturally-occurring source as it is found in nature, untouched,unmodified by the human hand. Accordingly, a naturally occurringcomposition is, e.g., one that is produced by an organism unmodifiedwith respect to the cellulolytic or hemicelluloytic enzymes such thatthe ratio or levels of the component enzymes are unaltered from thatproduced by the native organism in its native environment. A“non-naturally occurring composition,” on the other hand, refers to acomposition produced by: (1) combining component cellulolytic orhemicelluloytic enzymes either in a naturally occurring ratio or anon-naturally occurring, i.e., altered, ratio; or (2) modifying anorganism to express, overexpress or underexpress one or more endogeneousor exogenous enzymes; or (3) modifying an organism such that at leastone endogenous enzyme is deleted. A “non-naturally occurringcomposition” also refers to a composition produced by anaturally-occurring, unmodified organism, but cultured in a man-mademedium or environment that is different from the organism's nativeenvironment such that the amounts of enzymes in the composition differfrom those existing in a composition made by a native organism grown inits native habitat.

Any one of GH61 endoglucanase polypeptides or a variant thereof may beused in any of the compositions described herein. A suitable GH61endoglucanase may include one of the polypeptides shown in FIG. 1 of thepresent disclosure. Suitable GH61 endoglucanases include those that arerepresented by their GenBank Accession Numbers CAB97283.2, CAD70347.1,CAD21296.1, CAE81966.1, CAF05857.1, EAA26873.1, EAA29132.1, EAA30263.1,EAA33178.1, EAA33408.1, EAA34466.1, EAA36362.1, EAA29018.1, andEAA29347.1, or St61 from S. thermophilum 24630, St61A from S.thermophilum 23839c, St61B from S. thermophilum 46583, St61D from S.thermophilum 80312, Afu61a from A. fumigatus Afu3g03870 (NCBI Ref:XP_(—)748707), an endoglucanase of NCBI Ref: XP_(—)750843.1 from A.fumigatus Afu6g09540, an endoglucanase of A. fumigatus EDP47167, anendoglucanase of T. terrestris 16380, an endoglucanase of T. terrestris155418, an endoglucanase of T. terrestris 68900, Cg61A (EAQ86340.1) fromC. globosum, T. reesei Eg7, T. reesei Eg4, and an endoglucanase withGenBank Accession: XP_(—)752040 from A. fumigatus Af293. In someaspects, the polypeptide having GH61/endoglucanase activity (e.g.,isolated polypeptide) is a variant of GH61 endoglucanase or EG IV.

In some aspects, the polypeptide having GH61/endoglucanase activity(including a variant of GH61 endoglucanase) is one comprising any one ofSEQ ID NOs: 1-29 and 148, or one that comprises a polypeptide having atleast about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 92.5%, 95%, 96%, 97%,98%, or 99% sequence identity to any one of SEQ ID NOs: 1-29 and 148. Insome aspects, the polypeptide having GH61/endoglucanase activity(including a variant of GH61 endoglucanase) may comprise at least onemotif (at least any of 2, 3, 4, 5, 6, 7, or 8) selected from SEQ IDNOs:84-91. It may comprise one or more sequence motif(s) selected fromthe group consisting of: (1) SEQ ID NOs:84 and 88; (2) SEQ ID NOs:85 and88; (3) SEQ ID NO:86; (4) SEQ ID NO:87; (5) SEQ ID NOs:84, 88 and 89;(6) SEQ ID NOs:85, 88, and 89; (7) SEQ ID NOs: 84, 88, and 90; (8) SEQID NOs: 85, 88 and 90; (9) SEQ ID NOs:84, 88 and 91; (10) SEQ ID NOs:85, 88 and 91; (11) SEQ ID NOs: 84, 88, 89 and 91; (12) SEQ ID NOs: 84,88, 90 and 91; (13) SEQ ID NOs: 85, 88, 89 and 91: and (14) SEQ ID NOs:85, 88, 90 and 91.

In some aspects of any one of the compositions or methods describedherein, the polypeptide having GH61/endoglucanase activity (including avariant of GH61 endoglucanase) may have at least about 60% (e.g., atleast about any of 60%, 65%, 70%, 75%, 80%, 85%, 88%, 90%, 92.5%, 95%,96%, 97%, 98%, or 99%) sequence identity to residues 22 to 344 of SEQ IDNO:27. In some aspects, the polypeptide or a variant thereof comprisesresidues corresponding to at least about 5 residues (e.g., at leastabout any of 6, 7, 8, 9, 10, 11, or 12) of H22, D61, G63, C77, H107,R177, E179, H184, Q193, C198, Y195, and Y232 of SEQ ID NO:27. In someaspects, the polypeptide or a variant thereof comprises residuescorresponding to H22, D61, G63, C77, H107, R177, E179, H184, Q193, C198,Y195, and Y232 of SEQ ID NO:27. In some aspects, the polypeptide or avariant thereof comprises residues corresponding to at least 5 residues(e.g., at least about any of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, or 19) of G313, Q314, C315, G316, G317, S321, G322, P323, T324,C326, A327, T331, C332, N336, Y338, Y339, Q341, C342, and L343 of SEQ IDNO:27. In some aspects, the polypeptide or a variant thereof comprisesresidues corresponding to G313, Q314, C315, G316, G317, S321, G322,P323, T324, C326, A327, T331, C332, N336, Y338, Y339, Q341, C342, andL343 of SEQ ID NO:27. In some aspects, the polypeptide or a variantthereof comprises a CBM domain (e.g., functional CBM domain). In someaspects, the polypeptide or a variant thereof comprises a catalyticdomain (e.g., functional catalytic domain). In some aspects, thepolypeptide or a variant thereof is isolated. In some aspects, thepolypeptide or a variant thereof has endoglucanase activity.

In some aspects, the polypeptide having GH61/endoglucanase activity isendoglucanase IV, for example, a T. reesei Eg4 polypeptide or a variantthereof. For example, the disclosure provides non-naturally occurringcompositions comprising a T. reesei Eg4 polypeptide or a variantthereof. A variant of T. reesei Eg4 polypeptide can be any one of thevariants of T. reesei Eg4 polypeptide described herein. In some aspects,the polypeptide having GH61/endoglucanase activity includes amino acidsequence SEQ ID NO:27 or residues 22 to 344 of SEQ ID NO:27.

In some aspects, there is provided a composition comprising an isolated(or substantially purified) polypeptide having glycosyl hydrolase family61 (“GH61”)/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof). Methods of producing polypeptide, recovering the polypeptide,and isolating or purifying the polypeptide are known to one of skill inthe art.

In some aspects of any of the compositions or methods described herein,the polypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4or a variant thereof) is expressed from a host cell, wherein the nucleicacid encoding the polypeptide having GH61/endoglucanase activity hasbeen engineered into the host cell. In some aspects, the polypeptidehaving GH61/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof) is heterologous to the host cell expressing the polypeptidehaving GH61/endoglucanase activity.

The present disclosure provides compositions comprising a polypeptidehaving GH61/endoglucanase activity and comprising at least one cellulasepolypeptide and/or at least one hemicellulase polypeptide, or a mixturethereof. In some aspects, the composition comprises at least one (e.g.,at least 2, 3, 4, 5, 6, 7, or 8) cellulase polypeptide(s). In someaspects, the cellulase polypeptide is a polypeptide having endoglucanaseactivity, a polypeptide having cellobiohydrolase activity, or apolypeptide having β-glucosidase activity. In some aspects, thecomposition comprises at least one (e.g., at least 2, 3, 4, 5, 6, 7, or8) hemicellulase polypeptide(s). In some aspects, the hemicellulasepolypeptide is a polypeptide having xylanase activity, a polypeptidehaving β-xylosidase activity, or a polypeptide havingL-α-arabinofuranosidase activity. In some aspects, the compositionfurther comprises at least one (e.g., at least 2, 3, 4, 5, 6, 7, or 8)cellulase polypeptide(s) and at least one (e.g., at least 2, 3, 4, 5, 6,7, or 8) hemicellulase polypeptide(s). Varying amounts forpolypeptide(s) included in the compositions provided herein are providedbelow in “Amount of component(s) in compositions” section.

Cellulases and hemicellulases for use in accordance with the methods andcompositions of the disclosure can be obtained from, or producedrecombinantly from, inter alia, one or more of the following organisms:Crinipellis scapella, Macrophomina phaseolina, Myceliophthorathermophila, Sordaria fimicola, Volutella colletotrichoides, Thielaviaterrestris, Acremonium sp., Exidia glandulosa, Fomes fomentarius,Spongipellis sp., Rhizophlyctis rosea, Rhizomucor pusillus, Phycomycesniteus, Chaetostylum fresenii, Diplodia gossypina, Ulospora bilgramii,Saccobolus dilutellus, Penicillium verruculosum, Penicilliumchrysogenum, Thermomyces verrucosus, Diaporthe syngenesia,Colletotrichum lagenarium, Nigrospora sp., Xylaria hypoxylon, Nectriapinea, Sordaria macrospora, Thielavia thermophila, Chaetomium mororum,Chaetomium virscens, Chaetomium brasiliensis, Chaetomium cunicolorum,Syspastospora boninensis, Cladorrhinum foecundissimum, Scytalidiumthermophila, Gliocladium catenulatum, Fusarium oxysporum ssp.lycopersici, Fusarium oxysporum ssp. passiflora, Fusarium solani,Fusarium anguioides, Fusarium poae, Humicola nigrescens, Humicolagrisea, Panaeolus retirugis, Trametes sanguinea, Schizophyllum commune,Trichothecium roseum, Microsphaeropsis sp., Acsobolus stictoideus spej.,Poronia punctata, Nodulisporum sp., Trichoderma sp. (e.g., Trichodermareesei) and Cylindrocarpon sp.

In the present disclosure, the cellulase or hemicellulase may beprepared from any known microorganism cultivation method(s), resultingin the expression of enzymes capable of hydrolyzing a cellulosicmaterial. Fermentation may include shake flask cultivation, small- orlarge-scale fermentation, such as continuous, batch, fed-batch, or solidstate fermentations in laboratory or industrial fermenters performed ina suitable medium and under conditions allowing the cellulase to beexpressed or isolated. Generally, the microorganism is cultivated in acell culture medium suitable for production of enzymes capable ofhydrolyzing a cellulosic material. The cultivation takes place in asuitable nutrient medium comprising carbon and nitrogen sources andinorganic salts, using procedures known in the art. Suitable culturemedia, temperature ranges and other conditions suitable for growth andcellulase production are known in the art. As a non-limiting example,the normal temperature range for the production of cellulases by T.reesei is 24° C. to 28° C.

The present disclosure provides non-naturally occurring compositionscomprising a polypeptide having GH61/endoglucanase activity (e.g.,endoglucanase IV polypeptide such as T. reesei Eg4 polypeptide or avariant thereof), wherein the composition further comprises at least 1polypeptide having endoglucanase activity (e.g., at least 2, 3, 4, or 5polypeptides having endoglucanase activity), at least 1 polypeptidehaving cellobiohydrolase activity (e.g., at least 2, 3, 4, or 5polypeptides having cellobiohydrolase activity), at least 1 polypeptidehaving glucosidase activity (e.g., β-glucosidase) (e.g., at least 2, 3,4, or 5 polypeptides having β-glucosidase activity), at least 1polypeptide having xylanase activity (e.g., at least 2, 3, 4, or 5polypeptides having xylanase activity), at least 1 polypeptide havingxylosidase activity (e.g., β-xylosidase) (e.g., at least 2, 3, 4, or 5polypeptides having β-xylosidase activity), and/or at least 1polypeptide having arabinofuranosidase activity (e.g.,L-α-arabinofuranosidase) (e.g., at least 2, 3, 4, or 5 polypeptideshaving L-α-arabinofuranosidase activity). Varying amounts forpolypeptide(s) included in the compositions provided herein are providedbelow in “Amount of component(s) in compositions” section.

The present disclosure provides non-naturally occurring compositionscomprising whole cellulase comprising a polypeptide havingGH61/endoglucanase activity (e.g., whole cellulase enriched withendoglucanase IV polypeptide, such as, e.g., T. reesei Eg4 polypeptideor a variant thereof), wherein the composition further comprises atleast 1 polypeptide having endoglucanase activity (e.g., at least 2, 3,4, or 5 polypeptides having endoglucanase activity), at least 1polypeptide having cellobiohydrolase activity (e.g., at least 2, 3, 4,or 5 polypeptides having cellobiohydrolase activity), at least 1polypeptide having glucosidase activity (e.g., β-glucosidase) (e.g., atleast 2, 3, 4, or 5 polypeptides having β-glucosidase activity), atleast 1 polypeptide having xylanase activity (e.g., at least 2, 3, 4, or5 polypeptides having xylanase activity), at least one polypeptidehaving xylosidase activity (e.g., β-xylosidase) (e.g., at least 2, 3, 4,or 5 polypeptides having β-xylosidase activity), and/or at least onepolypeptide having arabinofuranosidase activity (e.g.,L-α-arabinofuranosidase) (e.g., at least 2, 3, 4, or 5 polypeptideshaving L-α-arabinofuranosidase activity). Varying amounts forpolypeptide(s) included in the compositions provided herein are providedbelow in “Amount of component(s) in compositions” section.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least 1 polypeptide having xylanase activity (e.g., T. reeseiXyn3, T. reesei Xyn2, AfuXyn2, AfuXyn5, or a variant thereof). In someaspects, the polypeptide having xylanase activity is T. reesei Xyn3. Thecomposition may further comprise at least 1 polypeptide havingβ-glucosidase activity (e.g., Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A,An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, and/or Tn3B). The composition mayfurther comprise at least 1 polypeptide having β-glucosidase activity(e.g., Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A,Vd3A, Pa3G, Tn3B, and/or a variant thereof). The composition may furthercomprise at least 1 polypeptide having cellobiohydrolase activity (e.g.,T. reesei CBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris7A, 7B, T. reesei CBH2, T. terrestris 6A, S. thermophile 6A, 6B, or avariant thereof). The composition may further comprise at least 1polypeptide having endoglucanase activity (e.g., T. reesei EG1 (or avariant thereof) and/or T. reesei EG2 (or a variant thereof)).

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least 1 polypeptide having β-glucosidase activity (e.g., Fv3C,Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G,Tn3B, or a variant thereof). The composition may comprise a polypeptidehaving GH61/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof) and at least 1 polypeptide (or at least 2 polypeptides) havingcellobiohydrolase activity (e.g., T. reesei CBH1, A. fumigatus 7A, 7B,C. globosum 7A, 7B, T. terrestris 7A, 7B, T. reesei CBH2, T. terrestris6A, S. thermophile 6A, 6B, or a variant thereof). The composition maycomprise a polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof) and further comprises at least 1polypeptide (or at least 2 polypeptides) having endoglucanase activity(e.g., T. reesei EG1 (or a variant thereof) and/or T. reesei EG2 (or avariant thereof)). The composition may comprise a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least 1 polypeptide (or at least two polypeptides) havingβ-xylosidase activity (e.g., Fv3A, Fv43A, Pf43A, Fv43D, Fv39A, Fv43E,Fo43A, Fv43B, Pa51A, Gz43A, and/or T. reesei Bxl1). The composition maycomprise a polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof) and at least 1 polypeptide (or at least2 polypeptides) having β-xylosidase activity (e.g., Fv3A, Fv43A, Pf43A,Fv43D, Fv39A, Fv43E, Fo43A, Fv43B, Pa51A, Gz43A, T. reesei Bxl1, and/ora variant thereof). The composition may comprise a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one polypeptide (at least 2 polypeptides) havingL-α-arabinofuranosidase activity (e.g., Af43A, Fv43B, Pf51A, Pa51A,Fv51A, or a variant thereof).

In some aspects, any of the polypeptides described herein (e.g.,polypeptide having endoglucanase activity, polypeptide havingcellobiohydrolase activity, polypeptide having glucosidase activity(e.g., β-glucosidase), polypeptide having xylanase activity, polypeptidehaving xylosidase activity (e.g., β-xylosidase), or polypeptide havingarabinofuranosidase activity (e.g., L-α-arabinofuranosidase)) may be acomponent of a whole cellulase such as a whole cellulase describedherein. Any of the polypeptides described herein may be produced byexpressing an endogenous or exogenous gene encoding the correspondingpolypeptide(s). The polypeptide(s) can be, in some circumstances,overexpressed or underexpressed.

Regarding any of the compositions described above, varying amounts forpolypeptide(s) included in the compositions are provided below in“Amount of component(s) in compositions” section.

Polypeptide Having Endoglucanase Activity

A polypeptide having endoglucanase activity includes a polypeptide thatcatalyzes the cleavage of internal β-1,4 linkages. Endoglucanase (“EG”)refers to a group of cellulase enzymes classified as EC 3.2.1.4. An EGenzyme hydrolyzes internal beta-1,4 glucosidic bonds of the cellulose.EG catalyzes endohydrolysis of 1,4-beta-D-glycosidic linkages incellulose, cellulose derivatives (for example, carboxy methylcellulose), lichenin, beta-1,4 bonds in mixed beta-1,3 glucans such ascereal beta-D-glucans or xyloglucans, and other plant materialcontaining cellulosic components. EG activity can be determined usingcarboxymethyl cellulose (CMC) hydrolysis according to the procedure ofGhose, 1987, Pure and Appl. Chem. 59: 257-268. In some aspects, at leastone polypeptide having endoglucanase activity includes T. reesei EG1(GenBank Accession No. HM641862.1) and/or T. reesei EG2 polypeptide(GenBank Accession No. ABA64553.1).

A thermostable T. terrestris endoglucanase (Kvesitadaze et al., AppliedBiochem. Biotech. 1995, 50:137-143) is, in another example, used in themethods and compositions of the present disclosure. Moreover, a T.reesei EG3 (GenBank Accession No. AAA34213.1) (Okada et al. Appl.Environ. Microbiol. 1988, 64:555-563), EG5 (GenBank Accession No.AAP57754) (Saloheimo et al. Molecular Microbiology 1994, 13:219-228),EG6 (FIG. 89A) (U.S. Patent Publication No. 20070213249), or EG7(GenBank Accession No. AAP57753) (U.S. Patent Publication No.20090170181), an A. cellulolyticus EI endoglucanase (Swiss-Prot entryP54583.1) (U.S. Pat. No. 5,536,655), a H. insolens endoglucanase V (EGV)(Protein Data Bank entry 4ENG), a S. coccosporum endoglucanase (FIG.89B) (U.S. Patent Publication No. 20070111278), an A. aculeatusendoglucanase F1-CMC (Swiss-Prot entry P22669.1) (Ooi et al. NucleicAcid Res. 1990, 18:5884), an A. kawachii IFO 4308 endoglucanase CMCase-1(Swiss-Prot entry Q96WQ8.1) (Sakamoto et al. Curr. Genet. 1995,27:435-439), an E. carotovara endoglucanase CelS (GenBank Accession No.AAA24817.1) (Saarilahti et al. Gene 1990, 90:9-14); or an A.thermophilum ALK04245 endoglucanase (U.S. Patent Publication No.20070148732) can also be used. Additional suitable endoglucanases aredescribed in, e.g., WO 91/17243, WO 91/17244, WO 91/10732, U.S. Pat. No.6,001,639. A polypeptide having endoglucanase activity may be a variantof any one of the endoglucases provided herein.

Polypeptide Having Cellobiohydrolase Activity

A polypeptide having cellobiohydrolase activity includes a polypeptidehaving 1,4-D-glucan cellobiohydrolase (E.C. 3.2.1.91) activity whichcatalyzes the hydrolysis of 1,4-beta-D-glucosidic linkages in cellulose,cellotetriose, or any beta-1,4-linked glucose containing polymer,releasing cellobiose from the ends of the chain. For purposes of thepresent invention, cellobiohydrolase activity can be determined byrelease of water-soluble reducing sugar from cellulose as measured bythe PHBAH method of Lever et al., 1972, Anal. Biochem. 47: 273-279. Adistinction between the exoglucanase mode of attack of acellobiohydrolase and the endoglucanase mode of attack can be made by asimilar measurement of reducing sugar release from substituted cellulosesuch as carboxymethyl cellulose or hydroxyethyl cellulose (Ghose, 1987,Pure & Appl. Chem. 59: 257-268). A true cellobiohydrolase will have avery high ratio of activity on unsubstituted versus substitutedcellulose (Bailey et al, 1993, Biotechnol. Appl. Biochem. 17: 65-76).

Suitable CBHs can be selected from A. bisporus CBH1 (Swiss ProtAccession No. Q92400), A. aculeatus CBH1 (Swiss Prot Accession No.059843), A. nidulans CBHA (GenBank Accession No. AF420019) or CBHB(GenBank Accession No. AF420020), A. niger CBHA (GenBank Accession No.AF156268) or CBHB (GenBank Accession No. AF156269), C. purpurea CBH1(Swiss Prot Accession No. 000082), C. carbonarum CBH1 (Swiss ProtAccession No. Q00328), C. parasitica CBH1 (Swiss Prot Accession No.Q00548), F. oxysporum CBH1 (Cel7A) (Swiss Prot Accession No. P46238), H.grisea CBH1.2 (GenBank Accession No. U50594), H. grisea var. thermoideaCBH1 (GenBank Accession No. D63515), CBHI.2 (GenBank Accession No.AF123441), or exol (GenBank Accession No. AB003105), M. albomyces Cel7B(GenBank Accession No. AJ515705), N. crassa CBHI (GenBank Accession No.X77778), P. funiculosum CBHI (Ce17A) (GenBank Accession No. AJ312295)(U.S. Patent Publication No. 20070148730), P. janthinellum CBHI (GenBankAccession No. S56178), P. chrysosporium CBH (GenBank Accession No.M22220), or CBHI-2 (Ce17D) (GenBank Accession No. L22656), T. emersoniiCBH1A (GenBank Accession No. AF439935), T. viride CBH1 (GenBankAccession No. X53931), or V. volvacea V14 CBH1 (GenBank Accession No.AF156693). A polypeptide having cellobiohydrolase activity may be avariant of any one of CBHs provided herein.

In some aspects, at least one polypeptide having cellobiohydrolaseactivity includes T. reesei CBH 1 (Swiss-Prot entry P62694.1) (or avariant thereof) and/or T. reesei CBH2 (Swiss-Prot entry P07987.1) (or avariant thereof) polypeptide. See Shoemaker et al. Bio/Technology 1983,1:691-696; see also Teeri et al. Bio/Technology 1983, 1:696-699, A.fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris 7A, 7B, which are T.reesei CBH1 homologs; T. terrestris 6A, S. thermophile 6A, 6B, which areT. reesei CBH2 homologs, or a variant thereof.

Polypeptide Having Glucosidase Activity

A polypeptide having glucosidase activity includes a polypeptide havingbeta-D-glucoside glucohydrolase (E.C. 3.2.1.21) activity which catalyzesthe hydrolysis of cellobiose with the release of beta-D-glucose. Forpurposes of the present invention, β-glucosidase activity may bemeasured by methods known in the art, e.g., HPLC. A polypeptide havingglucosidase activity includes members of certain GH families, including,without limitation, members of GH families 1, 3, 9 or 48, which catalyzethe hydrolysis of cellobiose to release β-D-glucose. A polypeptidehaving glucosidase activity includes β-glucosidase such as β-glucosidaseobtained from a number of microorganisms, by recombinant means, or bepurchased from commercial sources. Examples of β-glucosidases frommicroorganisms include, without limitation, ones from bacteria andfungi. For example, a β-glucosidase is suitably obtained from afilamentous fungus. In some aspects, at least one polypeptide havingglucosidase activity (e.g., β-glucosidase activity) is a T. reesei Bgl1polypeptide.

The β-glucosidases can be obtained, or produced recombinantly, from,inter alia, A. aculeatus (Kawaguchi et al. Gene 1996, 173: 287-288), A.kawachi (Iwashita et al. Appl. Environ. Microbiol. 1999, 65: 5546-5553),A. oryzae (WO 2002/095014), C. biazotea (Wong et al. Gene, 1998,207:79-86), P. funiculosum (WO 2004/078919), S. fibuligera (Machida etal. Appl. Environ. Microbiol. 1988, 54: 3147-3155), S. pombe (Wood etal. Nature 2002, 415: 871-880), or T. reesei (e.g., β-glucosidase 1(U.S. Pat. No. 6,022,725), β-glucosidase 3 (U.S. Pat. No. 6,982,159),β-glucosidase 4 (U.S. Pat. No. 7,045,332), β-glucosidase 5 (U.S. Pat.No. 7,005,289), β-glucosidase 6 (U.S. Publication No. 20060258554),β-glucosidase 7 (U.S. Publication No. 20060258554)). A polypeptidehaving β-glucosidases activity may be a variant of any one ofβ-glucosidases provided herein.

The β-glucosidase can be produced by expressing an endogenous orexogenous gene encoding a β-glucosidase. For example, β-glucosidase canbe secreted into the extracellular space e.g., by Gram-positiveorganisms (e.g., Bacillus or Actinomycetes), or a eukaryotic hosts(e.g., Trichoderma, Aspergillus, Saccharomyces, or Pichia). Theβ-glucosidase can be, in some circumstances, overexpressed orunderexpressed.

The β-glucosidase can also be obtained from commercial sources. Examplesof commercial β-glucosidase preparation suitable for use include, e.g.,T. reesei β-glucosidase in Accellerase® BG (Danisco US Inc., Genencor);NOVOZYM™ 188 (a β-glucosidase from A. niger); Agrobacterium sp.β-glucosidase, and T. maritima β-glucosidase from Megazyme (MegazymeInternational Ireland Ltd., Ireland.).

β-glucosidase activity can be determined by a number of suitable meansknown in the art, such as the assay described by Chen et al., inBiochimica et Biophysica Acta 1992, 121:54-60, wherein 1 pNPG denotes 1μmoL of Nitrophenol liberated from 4-nitrophenyl-β-D-glucopyranoside in10 min at 50° C. (122° F.) and pH 4.8.

Polypeptide Having Xylanase Activity

Xylanase activity may be measured by using colorimetric azo-birchwoodxylan assay (S-AXBL, Megazyme International Ireland Ltd., Ireland).

A polypeptide having xylanase activity may include Group A xylanases,selected from, e.g., Xyn, Xyn2, AfuXyn2, and/or AfuXyn5 polypeptide, ora variant thereof.

Any of the compositions described herein may optionally comprise one ormore xylanases in addition to or in place of the one or more Group Axylanases. Any xylanase (EC 3.2.1.8) can be used as the additional oneor more xylanases. Suitable xylanases include, e.g., C. saccharolyticumxylanase (Luthi et al. 1990, Appl. Environ. Microbiol. 56(9):2677-2683),T. maritima xylanase (Winterhalter & Liebel, 1995, Appl. Environ.Microbiol. 61(5):1810-1815), Thermatoga Sp. Strain FJSS-B.1 xylanase(Simpson et al. 1991, Biochem. J. 277, 413-417), B. circulans xylanase(BcX) (U.S. Pat. No. 5,405,769), A. niger xylanase (Kinoshita et al.1995, Journal of Fermentation and Bioengineering 79(5):422-428), S.lividans xylanase (Shareck et al. 1991, Gene 107:75-82; Morosoli et al.1986 Biochem. J. 239:587-592; Kluepfel et al. 1990, Biochem. J.287:45-50), B. subtilis xylanase (Bernier et al. 1983, Gene26(1):59-65), C. fimi xylanase (Clarke et al., 1996, FEMS MicrobiologyLetters 139:27-35), P. fluorescens xylanase (Gilbert et al. 1988,Journal of General Microbiology 134:3239-3247), C. thermocellum xylanase(Dominguez et al., 1995, Nature Structural Biology 2:569-576), B.pumilus xylanase (Nuyens et al. Applied Microbiology and Biotechnology2001, 56:431-434; Yang et al. 1998, Nucleic Acids Res. 16(14B):7187), C.acetobutylicum P262 xylanase (Zappe et al. 1990, Nucleic Acids Res.18(8):2179), or T. harzianum xylanase (Rose et al. 1987, J. Mol. Biol.194(4):755-756). A polypeptide having xylanase activity may be a variantof any one of the xylanases provided herein.

Polypeptide Having Xylosidase (e.g., β-Xylosidase) Activity

Xylosidase (e.g., β-xylosidase) activity may be measured by usingchromogenic substrate 4-nitrophenyl beta-D-xylopyranoside (pNPX,Sigma-Aldrich N2132).

A polypeptide having xylosidase (e.g., β-xylosidase) activity may be aGroup 1 β-xylosidase enzyme (e.g., Fv3A or Fv43A) or a Group 2β-xylosidase enzyme (e.g., Pf43A, Fv43D, Fv39A, Fv43E, Fo43A, Fv43B,Pa51A, Gz43A, T. reesei Bxl1, or a variant thereof). In some aspects,any of the composition provided herein may suitably comprise one or moreGroup 1 β-xylosidases and one or more Group 2 β-xylosidases.

Any of the composition provided herein such as the enzymeblends/compositions of the disclosure can optionally comprise one ormore β-xylosidases, in addition to or in place of the Group 1 and/orGroup 2 β-xylosidases above. Any β-xylosidase (EC 3.2.1.37) can be usedas the additional β-xylosidases. Suitable β-xylosidases include, forexample, T. emersonii Bxl1 (Reen et al. 2003, Biochem Biophys ResCommun. 305(3):579-85), G. stearothermophilus β-xylosidases (Shallom etal. 2005, Biochemistry 44:387-397), S. thermophilum β-xylosidases(Zanoelo et al. 2004, J. Ind. Microbiol. Biotechnol. 31:170-176), T.lignorum β-xylosidases (Schmidt, 1998, Methods Enzymol. 160:662-671), A.awamori β-xylosidases (Kurakake et al. 2005, Biochim. Biophys. Acta1726:272-279), A. versicolor β-xylosidases (Andrade et al. 2004, ProcessBiochem. 39:1931-1938), Streptomyces sp. β-xylosidases (Pinphanichakarnet al. 2004, World J. Microbiol. Biotechnol. 20:727-733), T. maritimaβ-xylosidases (Xue and Shao, 2004, Biotechnol. Lett. 26:1511-1515),Trichoderma sp. SY β-xylosidases (Kim et al. 2004, J. Microbiol.Biotechnol. 14:643-645), A. niger β-xylosidases (Oguntimein and Reilly,1980, Biotechnol. Bioeng. 22:1143-1154), or P. wortmanni β-xylosidases(Matsuo et al. 1987, Agric. Biol. Chem. 51:2367-2379). A polypeptidehaving xylosidase (e.g., β-xylosidase) activity may be a variant of anyone of the xylosidases provided herein.

Arabinofuranosidase activity may be measured by chromogenic substrate4-nitrophenyl alpha-L-arabinofuranoside (pNPA, Sigma-Aldrich N3641).

Any one of the compositions provided herein such as the enzymeblends/compositions of the disclosure can, for example, suitablycomprise at least one polypeptide having arabinofuranosidase activity(e.g., L-α-arabinofuranosidase activity) such asL-α-arabinofuranosidases. The L-α-arabinofuranosidase may be, forexample, Af43A, Fv43B, Pf51A, Pa51A, Fv51A, or a variant thereof.

The enzyme blends/compositions of the disclosure may optionally compriseone or more L-α-arabinofuranosidases in addition to or in place of theforegoing L-α-arabinofuranosidases. L-α-arabinofuranosidases (EC3.2.1.55) from any suitable organism can be used as the additionalL-α-arabinofuranosidases. Suitable L-α-arabinofuranosidases include,e.g., L-α-arabinofuranosidases of A. oryzae (Numan & Bhosle, J. Ind.Microbiol. Biotechnol. 2006, 33:247-260), A. sojae (Oshima et al. J.Appl. Glycosci. 2005, 52:261-265), B. brevis (Numan & Bhosle, J. Ind.Microbiol. Biotechnol. 2006, 33:247-260), B. stearothermophilus (Kim etal., J. Microbiol. Biotechnol. 2004, 14:474-482), B. breve (Shin et al.,Appl. Environ. Microbiol. 2003, 69:7116-7123), B. longum (Margolles etal., Appl. Environ. Microbiol. 2003, 69:5096-5103), C. thermocellum(Taylor et al., Biochem. J. 2006, 395:31-37), F. oxysporum (Panagiotouet al., Can. J. Microbiol. 2003, 49:639-644), F. oxysporum f. sp.dianthi (Numan & Bhosle, J. Ind. Microbiol. Biotechnol. 2006,33:247-260), G. stearothermophilus T-6 (Shallom et al., J. Biol. Chem.2002, 277:43667-43673), H. vulgare (Lee et al., J. Biol. Chem. 2003,278:5377-5387), P. chrysogenum (Sakamoto et al., Biophys. Acta 2003,1621:204-210), Penicillium sp. (Rahman et al., Can. J. Microbiol. 2003,49:58-64), P. cellulosa (Numan & Bhosle, J. Ind. Microbiol. Biotechnol.2006, 33:247-260), R. pusillus (Rahman et al., Carbohydr. Res. 2003,338:1469-1476), S. chartreusis, S. thermoviolacus, T. ethanolicus, T.xylanilyticus (Numan & Bhosle, J. Ind. Microbiol. Biotechnol. 2006,33:247-260), T. fusca (Tuncer and Ball, Folia Microbiol. 2003, (Praha)48:168-172), T. maritima (Miyazaki, Extremophiles 2005, 9:399-406),Trichoderma sp. SY (Jung et al. Agric. Chem. Biotechnol. 2005, 48:7-10),A. kawachii (Koseki et al., Biochim. Biophys. Acta 2006,1760:1458-1464), F. oxysporum f. sp. dianthi (Chacon-Martinez et al.,Physiol. Mol. Plant. Pathol. 2004, 64:201-208), T. xylanilyticus(Debeche et al., Protein Eng. 2002, 15:21-28), H. insolens, M. giganteus(Sorensen et al., Biotechnol. Prog. 2007, 23:100-107), or R. sativus(Kotake et al. J. Exp. Bot. 2006, 57:2353-2362). A polypeptide havingarabinofuranosidase activity may be a variant of any one of thearabinofuranosidases described herein.

In some aspects of any one of the compositions described herein, the atleast one polypeptide having endoglucanase activity comprises T. reeseiEG1 (or a variant thereof) and/or T. reesei EG2 (or a variant thereof).In some aspects of any one of the compositions described herein, the atleast one polypeptide having cellobiohydrolase (“CBH”) activitycomprises T. reesei CBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B, T.terrestris 7A, 7B, T. reesei CBH2, T. terrestris 6A, S. thermophile 6A,6B, or a variant thereof. In some aspects of any one of the compositionsdescribed herein, the at least one polypeptide having β-glucosidaseactivity comprises Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A,Gz3A, Nh3A, Vd3A, Pa3G, and/or Tn3B. In some aspects of any one of thecompositions described herein, the at least one polypeptide havingβ-glucosidase activity comprises Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B,Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A, Pa3G, Tn3B, and/or a variantthereof. In some aspects of any one of the compositions describedherein, the at least one polypeptide having xylanase activity comprisesT. reesei Xyn3, T. reesei Xyn2, AfuXyn2, and/or AfuXyn5. In some aspectsof any one of the compositions described herein, the at least onepolypeptide having xylanase activity comprises T. reesei Xyn3, T. reeseiXyn2, AfuXyn2, AfuXyn5, and/or a variant thereof. In some aspects of anyone of the compositions described herein, the at least one polypeptidehaving β-xylosidase activity is a Group 1 β-xylosidase or a Group 2β-xylosidase, wherein the Group 1 β-xylosidase comprises Fv3A, Fv43A, ora variant thereof, and the Group 2 β-xylosidase comprises Pf43A, Fv43D,Fv39A, Fv43E, Fo43A, Fv43B, Pa51A, Gz43A, T. reesei Bxl1, or a variantthereof. In some aspects, the at least one polypeptide havingβ-xylosidase activity comprises F. verticillioides Fv3A, F.verticillioides Fv43D, or a variant thereof. In some aspects of any oneof the compositions described herein, the at least one polypeptidehaving L-α-arabinofuranosidase activity comprises Af43A, Fv43B, Pf51A,Pa51A, and/or Fv51A. In some aspects of any one of the compositionsdescribed herein, the at least one polypeptide havingL-α-arabinofuranosidase activity comprises Af43A, Fv43B, Pf51A, Pa51A,Fv51A, and/or a variant thereof.

Whole Cellulase

Any of the compositions provided here such as enzyme blends/compositionsof the disclosure may comprise whole cellulase.

As used herein, a “whole cellulase” refers to either a naturallyoccurring or a non-naturally occurring cellulase-containing compositioncomprising at least 3 different enzyme types: (1) an endoglucanase, (2)a cellobiohydrolase, and (3) a β-glucosidase, or comprising at least 3different enzymatic activities: (1) an endoglucanase activity, whichcatalyzes the cleavage of internal β-1,4 linkages, resulting in shorterglucooligosaccharides, (2) a cellobiohydrolase activity, which catalyzesan “exo”-type release of cellobiose units (β-1,4 glucose-glucosedisaccharide), and (3) a β-glucosidase activity, which catalyzes therelease of glucose monomer from short cellooligosaccharides (e.g.,cellobiose). The whole cellulase may comprise at least one polypeptidehaving endoglucanase activity (e.g., EG2 (or a variant thereof) and/orEG4 (or a variant thereof)), at least one polypeptide havingcellobiohydrolase activity (e.g., CBH1 (or a variant thereof) and/orCBH2 (or a variant thereof)), and at least one polypeptide havingβ-glucosidase activity (e.g., Bgl1 or a variant thereof).

A “naturally occurring cellulase-containing” composition is one producedby a naturally occurring source, which comprises one or morecellobiohydrolase-type, one or more endoglucanase-type, and one or moreβ-glucosidase-type components or activities, wherein each of thesecomponents or activities is found at the ratio and level produced innature, untouched by the human hand. Accordingly, a naturally occurringcellulase-containing composition is, for example, one that is producedby an organism unmodified with respect to the cellulolytic enzymes suchthat the ratio or levels of the component enzymes are unaltered fromthat produced by the native organism in nature. A “non-naturallyoccurring cellulase-containing composition” refers to a compositionproduced by: (1) combining component cellulolytic enzymes either in anaturally occurring ratio or a non-naturally occurring, i.e., altered,ratio; or (2) modifying an organism to overexpress or underexpress oneor more cellulolytic enzymes; or (3) modifying an organism such that atleast one cellulolytic enzyme is deleted. A “non-naturally occurringcellulase containing” composition can also refer to a compositionresulting from adjusting the culture conditions for anaturally-occurring organism, such that the naturally-occurring organismgrows under a non-native condition, and produces an altered level orratio of enzymes. Accordingly, in some embodiments, the whole cellulasepreparation of the present disclosure can have one or more EGs and/orCBHs and/or β-glucosidases deleted and/or overexpressed.

In some aspects, there is provided a non-naturally occurring compositioncomprising a polypeptide having GH61/endoglucanase activity (e.g.,endoglucanase IV polypeptide such as T. reesei Eg4 polypeptide or avariant thereof) or a non-naturally occurring composition comprising apolypeptide having GH61/endoglucanase activity (e.g., whole cellulaseenriched with endoglucanase IV polypeptide such as T. reesei Eg4polypeptide or a variant thereof), wherein the composition furthercomprises a whole cellulase, at least 1 polypeptide having endoglucanaseactivity (e.g., at least 2, 3, 4, or 5 polypeptides having endoglucanaseactivity), at least 1 polypeptide having cellobiohydrolase activity(e.g., at least 2, 3, 4, or 5 polypeptides having cellobiohydrolaseactivity), at least 1 polypeptide having glucosidase activity (e.g.,β-glucosidase) (e.g., at least 2, 3, 4, or 5 polypeptides havingβ-glucosidase activity), at least 1 polypeptide having xylanase activity(e.g., at least 2, 3, 4, or 5 polypeptides having xylanase activity), atleast 1 polypeptide having xylosidase activity (e.g., β-xylosidase)(e.g., at least 2, 3, 4, or 5 polypeptides having β-xylosidaseactivity), and/or at least 1 polypeptide having arabinofuranosidaseactivity (e.g., L-α-arabinofuranosidase) (e.g., at least 2, 3, 4, or 5polypeptides having L-α-arabinofuranosidase activity). The polypeptideshaving various enzyme activities are described above.

In some aspects, the whole cellulase comprises at least 1 polypeptidehaving endoglucanase activity such as T. reesei EG1, T. reesei EG2, or avariant thereof. In some aspects, the whole cellulase comprises at leastone polypeptide having cellobiohydrolase activity such as T. reeseiCBH1, T. reesei CBH2, or a variant thereof. In some aspects, the wholecellulase comprises at least 1 polypeptide having β-glucosidase activitysuch as Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A,Nh3A, Vd3A, Pa3G, Tn3B, or a variant thereof.

In the present disclosure, a whole cellulase preparation can be from anymicroorganism that is capable of hydrolyzing a cellulosic material. Insome embodiments, the whole cellulase preparation is a fungal orbacterial whole cellulase. For example, the whole cellulase preparationcan be from an Acremonium, Aspergillus, Chrysosporium, Emericella,Fusarium, Humicola, Mucor, Myceliophthora, Neurospora, Penicillium,Scytalidium, Thielavia, Tolypocladium, Trichoderma, or yeast species.

The whole cellulase preparation may be, e.g., an Aspergillus aculeatus,Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus,Aspergillus nidula vs, Aspergillus niger, or Aspergillus oryzae wholecellulase. Moreover, the whole cellulase preparation may be a Fusariumbactridioides, Fusarium cerealis, Fusarium crookwellenσe, Fusariumculmorum, Fusarium graminearum, Fusarium graminum, Fusariumheterosporum, Fusarium negundi, Fusarium oxysporum, Fusariumreticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum,Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum,Fusarium trichothecioides, or Fusarium venenatum whole cellulasepreparation. The whole cellulase preparation may also be a Chrysosporiumlucknowence, Humicola insolens, Humicola lanuginosa, Mucor miehei,Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum,Penicillium funiculosum, Scytalidium thermophilum, or Thielaviaterrestris whole cellulase preparation. The whole cellulase preparationmay also be a Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, Trichoderma reesei (e.g., RL-P37 (Sheir-Neiss G et al.Appl. Microbiol. Biotechnology, 1984, 20, pp. 46-53), QM9414 (ATCC No.26921), NRRL 15709, ATCC 13631, 56764, 56466, 56767), or a Trichodermaviride (e.g., ATCC 32098 and 32086) whole cellulase preparation.

The whole cellulase preparation can be integrated strain T. reesei H3Aor H3A/Eg4 #27 (as described in the Examples herein) preparation.

The whole cellulase preparation can suitably be a T. reesei RutC30 wholecellulase preparation, which is available from the American Type CultureCollection as T. reesei ATCC 56765. For example, the whole cellulasepreparation can also suitably be a whole cellulase of P. funiculosum,which is available from the American Type Culture Collection as P.funiculosum ATCC Number: 10446.

The whole cellulase preparation can also be obtained from commercialsources. Examples of commercial cellulase preparations suitable for usein the methods and compositions of the present disclosure include, forexample, CELLUCLAST™ and Cellic™ (Novozymes A/S) and LAMINEX™ BG,IndiAge™ 44L, Primafast™ 100, Primafast™ 200, Spezyme™ CP, Accellerase®1000 and Accellerase® 1500 (Danisco US. Inc., Genencor).

Suitable whole cellulase preparations can be made using any knownmicroorganism cultivation methods, especially fermentation, resulting inthe expression of enzymes capable of hydrolyzing a cellulosic material.As used herein, “fermentation” refers to shake flask cultivation, small-or large-scale fermentation, such as continuous, batch, fed-batch, orsolid state fermentations in laboratory or industrial fermentersperformed in a suitable medium and under conditions that allow thecellulase and/or enzymes of interest to be expressed and/or isolated.Generally the microorganism is cultivated in a cell culture mediumsuitable for production of enzymes capable of hydrolyzing a cellulosicmaterial. The cultivation takes place in a nutrient medium comprisingcarbon and nitrogen sources and inorganic salts, using known proceduresand variations. Culture media, temperature ranges and other conditionsfor growth and cellulase production are known. As a non-limitingexample, a typical temperature range for the production of cellulases byT. reesei is 24° C. to 28° C.

The whole cellulase preparation can be used as it is produced byfermentation with no or minimal recovery and/or purification. In thatsense, the whole cellulase preparation can be used in a whole brothformulation. For example, once cellulases are secreted into the cellculture medium, the cell culture medium containing the cellulases can beused directly. The whole cellulase preparation can comprise theunfractionated contents of fermentation material, including the spentcell culture medium, extracellular enzymes and cells. On the other hand,the whole cellulase preparation can also be subject to furtherprocessing in a number of routine steps, e.g., precipitation,centrifugation, affinity chromatography, filtration, or the like. Forexample, the whole cellulase preparation can be concentrated, and thenused without further purification. The whole cellulase preparation can,e.g., be formulated to comprise certain chemical agents that decreasecell viability or kill the cells after fermentation. The cells can forexample be lysed or permeabilized using known methods.

The endoglucanase activity of the whole cellulase preparation can bedetermined using carboxymethyl cellulose (CMC) as a substrate. Asuitable assay measures the production of reducing ends created by theenzyme mixture acting on CMC wherein 1 unit is the amount of enzyme thatliberates 1 μmoL of product/min (Ghose, T. K., Pure & Appl. Chem. 1987,59, pp. 257-268).

The whole cellulase may be enriched with a polypeptide havingGH61/endoglucanase activity, e.g., an EG IV-enriched (such as, e.g.,enriched with T. reesei Eg4 polypeptide or a variant thereof) cellulase.The EG IV-enriched whole cellulase generally comprises an EG IVpolypeptide (such as, e.g., T. reesei Eg4 polypeptide or a variantthereof) and a whole cellulase preparation. The EG IV-enriched wholecellulase compositions can be produced by recombinant means. Forexample, such a whole cellulase preparation can be achieved byexpressing an EG IV in a microorganism capable of producing a wholecellulase. The EG IV-enriched whole cellulase composition can also,e.g., comprise a whole cellulase preparation and an EG IV (such as,e.g., T. reesei Eg4 polypeptide or a variant thereof). For instance, theEG IV-enriched (e.g., enriched with T. reesei Eg4 polypeptide or avariant thereof) whole cellulase composition can suitably comprise atleast 0.1 wt. %, 1 wt. %, 2 wt. %, 5 wt. %, 7 wt. %, 10 wt. %, 15 wt. %or 20 wt. %, and up to 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, or 50 wt.% EG IV based on the total weight of proteins in that blend/composition.

The whole cellulase can be a β-glucosidase-enriched cellulase. Theβ-glucosidase-enriched whole cellulase generally comprises aβ-glucosidase and a whole cellulase preparation. Theβ-glucosidase-enriched whole cellulase compositions can be produced byrecombinant means. For example, such a whole cellulase preparation canbe achieved by expressing a β-glucosidase in a microorganism capable ofproducing a whole cellulase The β-glucosidase-enriched whole cellulasecomposition can also, e.g., comprise a whole cellulase preparation and aβ-glucosidase. For instance, the β-glucosidase-enriched whole cellulasecomposition can suitably comprise at least 0.1 wt. %, 1 wt. %, 2 wt. %,5 wt. %, 7 wt. %, 10 wt. %, 15 wt. % or 20 wt. %, and up to 25 wt. %, 30wt. %, 35 wt. %, 40 wt. %, or 50 wt. % β-glucosidase based on the totalweight of proteins in that blend/composition.

Certain fungi produce complete cellulase systems, includingexo-cellobiohydrolases or CBH-type cellulases, endoglucanases or EG-typecellulases and β-glucosidase or BG-type cellulases (Schulein, 1988).However, sometimes these systems lack CBH-type cellulases, e.g.,bacterial cellulases also typically include little or no CBH-typecellulases. In addition, it has been shown that the EG components andCBH components synergistically interact to more efficiently degradecellulose. See, e.g., Wood, 1985. The different components, i.e., thevarious endoglucanases and exocellobiohydrolases in a multi-component orcomplete cellulase system, generally have different properties, such asisoelectric point, molecular weight, degree of glycosylation, substratespecificity and enzymatic action patterns.

In some aspects, the cellulase is used as is produced by fermentationwith no or minimal recovery and/or purification. For example, oncecellulases are secreted by a cell into the cell culture medium, the cellculture medium containing the cellulases can be used. In some aspects,the whole cellulase preparation comprises the unfractionated contents offermentation material, including cell culture medium, extracellularenzymes and cells. Alternatively, the whole cellulase preparation can beprocessed by any convenient method, e.g., by precipitation,centrifugation, affinity, filtration or any other method known in theart. In some aspects, the whole cellulase preparation can beconcentrated, for example, and then used without further purification.In some aspects, the whole cellulase preparation comprises chemicalagents that decrease cell viability or kills the cells. In some aspects,the cells are lysed or permeabilized using methods known in the art.

A composition is provided comprising a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and further comprising at least one cellulase polypeptide and/or atleast one hemicellulase polypeptide, wherein the cellulase polypeptideand/or the hemicellulase polypeptide is heterologous to the host cellexpressing the cellulase polypeptide and/or the hemicellulasepolypeptide. In some aspects, there is provided a composition comprisinga polypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4 ora variant thereof) and further comprising at least 1 cellulasepolypeptide and/or at least 1 hemicellulase polypeptide, wherein thecellulase polypeptide and/or the hemicellulase polypeptide is expressedfrom a host cell, and wherein cellulase polypeptide and/or ahemicellulase polypeptide is endogenous to the host cell. The cellulasepolypeptide may comprise a polypeptide having endoglucanase activity(e.g., T. reesei EG1 or a variant thereof, T. reesei EG2 or a variantthereof), a polypeptide having cellobiohydrolase activity (e.g., T.reesei CBH1, A. fumigatus 7A, 7B, C. globosum 7A, 7B, T. terrestris 7A,7B, T. reesei CBH2, T. terrestris 6A, S. thermophile 6A, 6B, or avariant thereof), or a polypeptide having β-glucosidase activity (e.g.,Fv3C, Pa3D, Fv3G, Fv3D, Tr3A, Tr3B, Te3A, An3A, Fo3A, Gz3A, Nh3A, Vd3A,Pa3G, Tn3B, or a variant thereof). The hemicellulase polypeptide maycomprise a polypeptide having xylanase activity (e.g., T. reesei Xyn3,T. reesei Xyn2, AfuXyn2, AfuXyn5, or a variant thereof), a havingβ-xylosidase activity (e.g., Fv3A, Fv43A, Pf43A, Fv43D, Fv39A, Fv43E,Fo43A, Fv43B, Pa51A, Gz43A, T. reesei Bxl1, or a variant thereof), or apolypeptide having L-α-arabinofuranosidase activity (e.g., Af43A, Fv43B,Pf51A, Pa51A, Fv51A, or a variant thereof).

In some aspects, the composition is from fermentation broth. Thecomposition may be from the fermentation broth of a strain, wherein anucleic acid encoding a polypeptide having GH61/endoglucanase activity(e.g., T. reesei Eg4 or a variant thereof) is heterologous to the hostcell expressing the polypeptide having GH61/endoglucanase activity(e.g., integrated into the strain or expressed from a vector in the hoststrain). The composition may be from the fermentation broth of anintegrated strain (e.g., H3A/Eg4, #27 as in Examples).

The composition comprising a polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof) may comprise wholecellulase. Thus, a composition is provided (e.g., a non-naturallyoccurring composition) comprising T. reesei Eg4 (or a variant thereof),T. reesei Bgl1 (or a variant thereof), T. reesei xyn3 (or a variantthereof), Fv3A (or a variant thereof), Fv43D (or a variant thereof), andFv51A (or a variant thereof).

In some aspects, the composition comprises isolated T. reesei Eg4. Insome aspects, the composition comprises at least one (at least 2, 3, 4,or 5) of isolated T. reesei Bgl1, isolated T. reesei xyn3, isolatedFv3A, isolated Fv43D, and isolated Fv51A.

In some aspects, the composition is from fermentation broth. In someaspects, the composition is from the fermentation broth of an integratedstrain (e.g., H3A/Eg4, #27 as described herein in the Examples). The T.reesei Eg4 or the nucleic acid encoding T. reesei Eg4 may beheterologous to the host cell expressing T. reesei Eg4. At least onenucleic acid encoding T. reesei Bgl1, T. reesei xyn3, Fv3A, Fv43D,Fv51A, or a variant thereof may be heterologous to the host cell such asthe host cell expressing T. reesei Eg4. In some aspects, at least onenucleic acid encoding T. reesei Bgl1, T. reesei xyn3, Fv3A, Fv43D,Fv51A, or a variant thereof is endogenous to the host cell such as thehost cell expressing T. reesei Eg4.

Regarding any of the compositions described above, varying amounts ofthe polypeptide(s) included in the compositions are described below in“Amount of component(s) in compositions” section.

Amount of Component(s) in Compositions

A non-naturally occurring composition comprising a polypeptide havingGH61/endoglucanase activity (or a non-naturally occurring compositioncomprising whole cellulase comprising a polypeptide havingGH61/endoglucanase activity) provided herein may comprise variouscomponents as described herein, wherein each component is present in thecomposition in various amount.

In some aspects of any one of the compositions or methods providedherein, the polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof) is present in the composition in anamount sufficient to increase the yield of fermentable sugar(s) fromhydrolysis of biomass material (e.g., by at least about any of 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) comparedto the yield in the absence of the polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof). Any one of thecompositions or methods provided herein, the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)may be present in the composition in an amount sufficient to reduce theviscosity of a biomass mixture during hydrolysis of a biomass material(e.g., by at least about any of 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 60%, 70%, 80%, or 90%) compared to the viscosity of thebiomass mixture during hydrolysis in the absence of the polypeptidehaving GH61/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof). The composition may further comprise at least 1 polypeptidehaving endoglucanase activity, at least 1 polypeptide havingcellobiohydrolase activity, at least 1 polypeptide having β-glucosidaseactivity, at least 1 polypeptide having xylanase activity, at least 1polypeptide having β-xylosidase activity, at least 1 polypeptide havingL-α-arabinofuranosidase activity, and/or whole cellulase, or a mixturethereof. The amount of polypeptide(s) having endoglucanase activity, theamount of polypeptide(s) having cellobiohydrolase activity, the amountof polypeptide(s) having β-glucosidase activity, the amount ofpolypeptide(s) having xylanase activity, the amount of polypeptide(s)having β-xylosidase activity, the amount of polypeptide(s) havingL-α-arabinofuranosidase activity, or the amount of whole cellulase issufficient to increase the yield of fermentable sugar(s) from hydrolysisof biomass material (e.g., by at least about any of 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) compared to theyield in the absence of the polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof), the polypeptide(s)having endoglucanase activity, the polypeptide(s) havingcellobiohydrolase activity, the polypeptide(s) having β-glucosidaseactivity, the polypeptide(s) having xylanase activity, thepolypeptide(s) having β-xylosidase activity, the polypeptide(s) havingL-α-arabinofuranosidase activity, or the whole cellulase. In someaspects, the amount of polypeptide(s) having endoglucanase activity, theamount of polypeptide(s) having cellobiohydrolase activity, the amountof polypeptide(s) having β-glucosidase activity, the amount ofpolypeptide(s) having xylanase activity, the amount of polypeptide(s)having β-xylosidase activity, the amount of polypeptide(s) havingL-α-arabinofuranosidase activity, or the amount of whole cellulase issufficient to reduce the viscosity of a biomass mixture duringhydrolysis of a biomass material (e.g., by at least about any of 5%,10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%)compared to the viscosity of a biomass mixture in the absence of thepolypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4 or avariant thereof), the polypeptide(s) having endoglucanase activity, thepolypeptide(s) having cellobiohydrolase activity, the polypeptide(s)having β-glucosidase activity, the polypeptide(s) having xylanaseactivity, the polypeptide(s) having β-xylosidase activity, thepolypeptide(s) having L-α-arabinofuranosidase activity, or the wholecellulase.

A polypeptide having GH61/endoglucanase activity (such as EG IVincluding T. reesei Eg4 polypeptide or a variant thereof) may be presentin any of the compositions described herein (such as in any of theenzyme blends/compositions provided herein) in an amount that is atleast about any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. %7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, or 50 wt. % of the totalweight of proteins in the composition. In some aspects, a polypeptidehaving GH61/endoglucanase activity (such as EG IV including, e.g., T.reesei Eg4 polypeptide or a variant thereof) may be present in any ofthe compositions described herein (such as in any of the enzymeblends/compositions provided herein) in an amount that is no more thanabout any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt.%, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %,25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65wt. %, 70 wt. %, 75 wt. %, or 80 wt. % of the total weight of proteinsin the composition. A polypeptide having GH61/endoglucanase activity(such as EG IV including, e.g., T. reesei Eg4 polypeptide or a variantthereof) may be present in any of the compositions described herein(such as in any of the enzyme blends/compositions provided herein) in anamount that has a range having upper limit and lower limit. For example,lower limit for a polypeptide having GH61/endoglucanase activity isabout any of 0.01 wt. %, 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 12 wt. %, 15 wt. %, 20 wt. %,25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, or 50 wt. % of the total weightof proteins in the composition. Upper limit for a polypeptide havingGH61/endoglucanase activity may be about any of 10 wt, %, 15 wt, %, 20wt. %, 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, 50 wt. %, 55 wt. %, 60wt. %, 65 wt. % or 70 wt. % of the total weight of proteins in thecomposition. In some aspects, a polypeptide having GH61/endoglucanaseactivity (such as EG IV including, e.g., T. reesei Eg4 polypeptide or avariant thereof) may be present in any of the compositions describedherein (such as in any of the enzyme blends/compositions providedherein) in an amount that is about any of 1 wt. %, 2 wt. %, 3 wt. %, 4wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %,12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, 50wt. %, 55 wt. %, 60 wt. %, 65 wt. %, 70 wt. %, 75 wt. %, or 80 wt. % ofthe total weight of proteins in the composition. The polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)may be present in about 10 wt. % or 12 wt. % of the total weight ofproteins in the composition. The composition may have at least twopolypeptides having endoglucanase activity (e.g., T. reesei Eg4, T.reesei Eg1, and/or T. reesei Eg2, or a variant thereof), where the totalamount of polypeptides having endoglucanase activity is about 0.1 toabout 50 wt. % (e.g., about 0.5 to about 45 wt. %, about 1 to about 30wt. %, about 2 to about 20 wt. %, about 5 to about 20 wt. %, or about 8to about 15 wt. %) of the total weight of proteins in the composition.The polypeptide having GH61/endoglucanase activity may be heterologousor endogenous to the host cell expressing the polypeptide havingGH61/endoglucanase activity. The polypeptide having GH61/endoglucanaseactivity included in the composition may be isolated.

In some aspects, the enzyme composition (e.g., the enzyme composition)described herein is whole cellulase composition comprising a polypeptidehaving GH61/endoglucanase activity. In some aspects, a polypeptidehaving GH61/endoglucanase activity (such as EG IV including, e.g., T.reesei Eg4 polypeptide or a variant thereof) may be present in an amountthat is at least about any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt.%, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, or 50 wt. % ofthe total weight of the whole cellulase. In some aspects, a polypeptidehaving GH61/endoglucanase activity (such as EG IV including, e.g., T.reesei Eg4 polypeptide or a variant thereof) may be present in an amountthat is no more than about any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %,15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55wt. %, 60 wt. %, 65 wt. %, 70 wt. %, 75 wt. %, or 80 wt. % of the totalweight of the whole cellulase. In some aspects, a polypeptide havingGH61/endoglucanase activity (such as EG IV including, e.g., T. reeseiEg4 polypeptide or a variant thereof) may be present in an amount thathas a lower limit of about any of 0.01 wt. %, 1 wt. %, 2 wt. %, 3 wt. %,4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 12 wt. %,15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, or 50 wt. %of the total weight of the whole cellulase and a upper limit of aboutany of 10 wt, %, 15 wt, %, 20 wt. %, 25 wt. %, 30 wt. %, 35 wt. %, 40wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. % or 70 wt. % of the totalweight of the whole cellulase. In some aspects, a polypeptide havingGH61/endoglucanase activity (such as EG IV including, e.g., T. reeseiEg4 polypeptide or a variant thereof) may be present in an amount thatis about any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 13 wt. %, 14 wt.%, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, 50 wt. %,55 wt. %, 60 wt. %, 65 wt. %, 70 wt. %, 75 wt. %, or 80 wt. % of thetotal weight of the whole cellulase. In some aspects, a polypeptidehaving GH61/endoglucanase activity (such as EG IV including, e.g., T.reesei Eg4 polypeptide or a variant thereof) is present in an amountthat is about 10 wt. % or 12 wt. % of the total weight of the wholecellulase.

In some aspects, any of the compostions provided herein may comprise atleast one polypeptide having endoglucanase activity (e.g., in additionto a polypeptide having GH61/endoglucanase activity) including T. reeseiEg1 or a variant thereof and/or T. reesei Eg2 or a variant thereof. Insome aspects, the total amount of the polypeptide(s) havingendoglucanase activity may be present in any of the compositionsdescribed herein (such as in any of the enzyme blends/compositionsprovided herein) in an amount that is at least about 1 wt. %, 2 wt. %, 3wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45wt. %, or 50 wt. % of the total weight of proteins in the composition.In some aspects, the total amount of the polypeptide(s) havingendoglucanase activity may be present in any of the compositionsdescribed herein (such as in any of the enzyme blends/compositionsprovided herein) in an amount that is no more than about any of 1 wt. %,2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %,10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. %, 70 wt. %, 75wt. %, or 80 wt. % of the total weight of proteins in the composition.In some aspects, the total amount of the polypeptide(s) havingendoglucanase activity may be present in any of the compositionsdescribed herein (such as in any of the enzyme blends/compositionsprovided herein) in an amount that has a range having upper limit andlower limit. For example, lower limit for the total amount of thepolypeptide(s) having endoglucanase activity is about any of 0.01 wt. %,1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9wt. %, 10 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40wt. %, 45 wt. %, or 50 wt. % of the total weight of proteins in thecomposition. Upper limit for the total amount of the polypeptide(s)having endoglucanase activity may be about any of 10 wt, %, 15 wt, %, 20wt. %, 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, 50 wt. %, 55 wt. %, 60wt. %, 65 wt. % or 70 wt. % of the total weight of proteins in thecomposition. In some aspects, the total amount of the polypeptide(s)having endoglucanase activity may be present in any of the compositionsdescribed herein (such as in any of the enzyme blends/compositionsprovided herein) in an amount that is about any of 1 wt. %, 2 wt. %, 3wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. %, 70 wt. %, 75 wt. %, or 80wt. % of the total weight of proteins in the composition.

In some aspects, any of the compostions provided herein may comprise oneor more polypeptide with various enzyme activity, such as polypeptide(s)having cellobiohydrolase activity, polypeptide(s) having glucosidaseactivity (e.g., β-glucosidase), polypeptide(s) having xylanase activity,polypeptide(s) having xylosidase activity, and/or polypeptide(s) havingarabinofuranosidase activity. In some aspects, there may be multiplepolypeptides having the same enzyme activity. Each of the polypeptidesmentioned above (or the total amount of the polypeptides having aspecific enzyme activity, e.g., total amount of the polypeptides havingcellobiohydrolase activity, glucosidase activity (e.g., β-glucosidase),xylanase activity, xylosidase activity, or arabinofuranosidase activity)may be present in any of the compositions described herein (such as inany of the enzyme blends/compositions provided herein) in an amount thatis at least about any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %,20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, or 50 wt. % of thetotal weight of proteins in the composition. In some aspects, each ofthe polypeptides mentioned above (or the total amount of thepolypeptides having a specific enzyme activity, e.g., total amount ofthe polypeptides having cellobiohydrolase activity, glucosidase activity(e.g., β-glucosidase), xylanase activity, xylosidase activity, orarabinofuranosidase activity) may be no more than about any of 1 wt. %,2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %,10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. %, 70 wt. %, 75wt. %, or 80 wt. % of the total weight of proteins in the composition.Each of the polypeptides mentioned above (or the total amount of thepolypeptides having a specific enzyme activity, e.g., total amount ofthe polypeptides having cellobiohydrolase activity, glucosidase activity(e.g., β-glucosidase), xylanase activity, xylosidase activity, orarabinofuranosidase activity) may be present in any of the compositionsdescribed herein (such as in any of the enzyme blends/compositionsprovided herein) in an amount that has a range having upper and lowerlimits. For example, lower limit for the total amount of thepolypeptide(s) having endoglucanase activity is about any of 0.01 wt. %,1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9wt. %, 10 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40wt. %, 45 wt. %, or 50 wt. % of the total weight of proteins in thecomposition. Upper limit may be about any of 10 wt, %, 15 wt, %, 20 wt.%, 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, 50 wt. %, 55 wt. %, 60 wt. %,65 wt. % or 70 wt. % of the total weight of proteins in the composition.In some aspects, each of the polypeptides mentioned above (or the totalamount of the polypeptides having a specific enzyme activity, e.g.,total amount of the polypeptides having cellobiohydrolase activity,glucosidase activity (e.g., β-glucosidase), xylanase activity,xylosidase activity, or arabinofuranosidase activity) may be present inany of the compositions described herein (such as in any of the enzymeblends/compositions provided herein) in an amount that is about any of 1wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. %, 70wt. %, 75 wt. %, or 80 wt. % of the total weight of proteins in thecomposition.

In some aspects, any of the compostions provided herein may furthercomprise whole cellulase. The whole cellulase may be present in any ofthe compositions described herein (such as in any of the enzymeblends/compositions provided herein) in an amount that is at least aboutany of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt.%, 30 wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. %,70 wt. %, 75 wt. %, 80 wt. %, 85 wt. %, 90 wt. %, or 95 wt. % of thetotal weight of proteins in the composition. The whole cellulase may bepresent in any of the compositions described herein (such as in any ofthe enzyme blends/compositions provided herein) in an amount that is nomore than about any of 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %,25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65wt. %, 70 wt. %, 75 wt. %, 80 wt. %, 85 wt. %, 90 wt. %, or 95 wt. % ofthe total weight of proteins in the composition. The whole cellulase maybe present in any of the compositions described herein (such as in anyof the enzyme blends/compositions provided herein) in an amount that isabout any of 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt.%, 8 wt. %, 9 wt. %, 10 wt. %, 11 wt. %, 12 wt. %, 15 wt. %, 20 wt. %,25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65wt. %, 70 wt. %, 75 wt. %, 80 wt. %, 85 wt. %, 90 wt. %, or 95 wt. % ofthe total weight of proteins in the composition.

In some aspects of any one of the compositions or methods providedherein, the polypeptide having cellobiohydrolase activity (e.g., T.reesei CBH1, T. reesei CBH2, or a variant thereof) is present in anamount that is about 0.1 to about 70 wt. % (e.g., about 0.5 to about 60wt. %, about 5 to about 70 wt. %, about 10 to about 60 wt. %, about 20to about 50 wt. %, or about 30 to about 50 wt. %) of the total weight ofproteins in the composition. In some aspects, the composition has atleast two polypeptides having cellobiohydrolase activity (e.g., T.reesei CBH1 (or a variant thereof) and T. reesei CBH2 (or a variantthereof)), wherein the total amount of polypeptides havingcellobiohydrolase activity is about 0.1 to about 70 wt. % (e.g., about0.5 to about 60 wt. %, about 5 to about 70 wt. %, about 10 to about 60wt. %, about 20 to about 50 wt. %, or about 30 to about 50 wt. %) of thetotal weight of proteins in the composition. The polypeptide havingcellobiohydrolase activity may be expressed from a nucleic acidheterologous or endogenous to the host cell. In some aspects, thepolypeptide having cellobiohydrolase activity included in thecomposition is isolated.

In some aspects of any one of the compositions or methods providedherein, the polypeptide having β-glucosidase activity (e.g., an Fv3C, aPa3D, an Fv3G, an Fv3D, a Tr3A, a Tr3B, a Te3A, an An3A, an Fo3A, aGz3A, an Nh3A, a Vd3A, a Pa3G, a Tn3B, or a variant thereof) is presentin an amount that is about 0.1 to about 50 wt. % (e.g., about 0.5 toabout 40 wt. %, about 1 to about 30 wt. %, about 2 to about 20 wt. %,about 5 to about 20 wt. %, or about 8 to about 15 wt. %) of the totalweight of proteins in the composition. In some aspects, the compositionhas at least two polypeptides having β-glucosidase activity, wherein thetotal amount of polypeptides having β-glucosidase activity is about 0.1to about 50 wt. % (e.g., about 0.5 to about 40 wt. % about 1 to about 30wt. %, about 2 to about 20 wt. %, about 5 to about 20 wt. %, or about 8to about 15 wt. %) of the total weight of proteins in the composition.The polypeptide having β-glucosidase activity may be expressed from anucleic acid heterologous or endogenous to the host cell. In someaspects, the polypeptide having β-glucosidase activity included in thecomposition is isolated.

Any one of the compositions or methods provided herein, the polypeptidehaving xylanase activity (e.g., T. reesei Xyn3, T. reesei Xyn2, anAfuXyn2, an AfuXyn5, or a variant thereof) may be present in an amountthat is about 0.1 to about 50 wt. % (e.g., about 0.5 to about 40 wt. %,about 1 to about 40 wt. %, about 4 to about 30 wt. %, about 5 to about20 wt. %, or about 8 to about 15 wt. %) of the total weight of proteinsin the composition. The composition may have at least 2 polypeptideshaving xylanase activity, wherein the total amount of polypeptideshaving xylanase activity is about 0.1 to about 50 wt. % (e.g., about 0.5to about 40 wt. %, about 1 to about 40 wt. %, about 4 to about 30 wt. %,about 5 to about 20 wt. %, or about 8 to about 15 wt. %) of the totalweight of proteins in the composition. The polypeptide having xylanaseactivity may be expressed from a nucleic acid heterologous or endogenousto the host cell. The polypeptide having xylanase activity included inthe composition may be isolated.

Any one of the compositions or methods provided herein, the polypeptidehaving L-α-arabinofuranosidase activity (e.g., an Af43A, an Fv43B, aPf51A, a Pa51A, an Fv51A, or a variant thereof) may be present in anamount that is about 0.1 to about 50 wt. % (e.g., about 0.5 to about 45wt. %, about 1 to about 40 wt. %, about 2 to about 30 wt. %, about 4 toabout 20 wt. %, or about 5 to about 15 wt. %) of the total weight ofenzymes in the composition. The composition may have at least 2polypeptides having L-α-arabinofuranosidase activity, wherein the totalamount of polypeptides having L-α-arabinofuranosidase activity is about0.1 to about 50 wt. % (e.g., about 0.5 to about 45 wt. %, about 1 toabout 40 wt. %, about 2 to about 30 wt. %, about 4 to about 20 wt. %, orabout 5 to about 15 wt. %) of the total weight of proteins in thecomposition. The polypeptide having L-α-arabinofuranosidase activity maybe expressed from a nucleic acid heterologous or heterologous to thehost cell. The polypeptide having L-α-arabinofuranosidase activityincluded in the composition may be isolated.

Any one of the compositions or methods provided herein, the polypeptidehaving β-xylosidase activity (e.g., Fv3A, Fv43A, a Pf43A, an Fv43D, anFv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51A, a Gz43A, a T. reesei Bxl1,or a variant thereof) may be present in an amount that is about 0.1 toabout 50 wt. % (e.g., about 0.5 to about 45 wt. %, about 1 to about 40wt. %, about 4 to about 35 wt. %, about 5 to about 25 wt. %, or about 5to about 20 wt. %) of the total weight of enzymes in the composition.The composition may have at least 2 polypeptides having β-xylosidaseactivity, wherein the total amount of polypeptides having β-xylosidaseactivity is about 0.1 to about 50 wt. % (e.g., about 0.5 to about 45 wt.%, about 1 to about 40 wt. %, about 4 to about 35 wt. %, about 5 toabout 25 wt. %, or about 5 to about 20 wt. %) of the total weight ofproteins in the composition. The polypeptide having β-xylosidaseactivity may be expressed from a nucleic acid heterologous or endogenousto the host cell. The polypeptide having β-xylosidase activity includedin the composition may be isolated.

Any one of the compositions or methods provided herein, the wholecellulase in the composition may be about 0.1 to about 100 wt. % (e.g.,about 1 to about 95 wt. %, about 5 to about 90 wt. %, about 10 to about85 wt. %, about 20 to about 80 wt. %, or about 30 to about 75 wt. %) ofthe total weight of proteins in the composition. The whole cellulase maycomprise at least 1 polypeptide having endoglucanase activity (such asT. reesei Eg4 or a variant thereof, T. reesei Eg1 or a variant thereof,T. reesei Eg2 or a variant thereof) expressed from a nucleic acidheterologous or endogenous to the host cell. The whole cellulase maycomprise at least 1 polypeptide having cellobiohydrolase activity (e.g.,T. reesei CBH1 or a variant thereof, T. reesei CBH2 or a variantthereof) expressed from a nucleic acid heterologous or endogenous to thehost cell. The whole cellulase may comprise at least one polypeptidehaving β-glucosidase activity (e.g., an Fv3C, a Pa3D, an Fv3G, an Fv3D,a Tr3A, a Tr3B, a Te3A, an An3A, an Fo3A, a Gz3A, an Nh3A, a Vd3A, aPa3G, a Tn3B, or a variant thereof) expressed from a nucleic acidheterologous or endogenous to the host cell.

In some aspects, the composition of the invention is capable ofconverting a biomass material into fermentable sugar(s) (e.g., glucose,xylose, arabinose, and/or cellobiose). In some aspects, the compositionis capable of achieving at least 0.1 (e.g., 0.1 to 0.4) fraction productas determined by the calcofluor assay.

In some aspects, the composition comprises the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and further comprises at least one cellulase polypeptide and/or at leastone hemicellulase polypeptide, wherein the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one cellulase polypeptide and/or at least one hemicellulasepolypeptide are mixed together before contacting a biomass material.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and further comprises at least one cellulase polypeptide and/or at leastone hemicellulase polypeptide, wherein the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one cellulase polypeptide and/or at least one hemicellulasepolypeptide are added to a biomass material at different times (e.g., apolypeptide having GH61/endoglucanase activity is added to a biomassmaterial before or after the at least one cellulase polypeptide and/orat least one hemicellulase polypeptide is added to the biomassmaterial).

In some aspects, the composition comprising a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)is a mixture comprising a biomass material, e.g., the composition is ahydrolysis mixture, a fermentation mixture, or a saccharificationmixture. Such mixture may further include fermentable sugar(s).

Other Components

The enzyme compositions of the disclosure may suitably further comprise1 or more accessory proteins. Examples of accessory proteins include,without limitation, mannanases (e.g., endomannanases, exomannanases, andβ-mannosidases), galactanases (e.g., endo- and exo-galactanases),arabinases (e.g., endo-arabinases and exo-arabinases), ligninases,amylases, glucuronidases, proteases, esterases (e.g., ferulic acidesterases, acetyl xylan esterases, coumaric acid esterases or pectinmethyl esterases), lipases, other glycoside hydrolases, xyloglucanases,CIP1, CIP2, swollenins, expansins, and cellulose disrupting proteins.For example, the cellulose disrupting proteins are cellulose bindingmodules.

Methods and Processes

The disclosure provides methods and processes for biomasssaccharification, using enzymes, enzyme blends/compositions of thedisclosure. In particular, the disclosure provides methods and processesfor using any one of the polypeptides or compositions provided hereinfor hydrolyzing a biomass material. Further, the disclosure providesmethods of using any one of the polypeptides or compositions providedherein for reducing the viscosity of a biomass mixture (e.g., a biomassmixture containing biomass substrate and enzyme during saccharificationprocess). In some aspects, there are provided methods of hydrolyzing abiomass material comprising contacting the biomass material with anon-naturally occurring composition comprising a polypeptide havingGH61/endoglucanase activity. In some aspects, the polypeptide is in anamount sufficient to hydrolyze the biomass material.

The term “biomass,” as used herein, refers to any composition comprisingcellulose and/or hemicellulose (including lignin in lignocellulosicbiomass materials). As used herein, biomass includes, withoutlimitation, seeds, grains, tubers, plant waste or byproducts of foodprocessing or industrial processing (e.g., stalks), corn (including,e.g., cobs, stover, and the like), grasses (including, e.g., Indiangrass, such as Sorghastrum nutans; or, switchgrass, e.g., Panicumspecies, such as Panicum virgatum), perennial canes (e.g., giant reeds),wood (including, e.g., wood chips, processing waste), paper (includingpaper waste), pulp, and recycled paper (including, e.g., newspaper,printer paper, and the like). Other biomass materials include, withoutlimitation, potatoes, soybean (e.g., rapeseed), barley, rye, oats,wheat, beets, and sugar cane bagasse. Suitable lignocellulosic biomassmaterials include, without limitation, seeds, grains, tubers, plantwaste or byproducts of food processing or industrial processing (e.g.,stalks), corn (including, e.g., cobs, stover, and the like), grasses(e.g., Indian grass, such as Sorghastrum nutans; or, switchgrass, e.g.,Panicum species, such as Panicum virgatum), perennial canes, e.g., giantreeds, wood (including, e.g., wood chips, processing waste), paper,pulp, recycled paper (e.g., newspaper), wood pulp, or sawdust. Examplesof grasses include, without limitation, Indian grass or switchgrass.Examples of reeds include, without limitation, certain perennial canessuch as giant reeds. Examples of paper waste include, withoutlimitation, discarded or used photocopy paper, computer printer paper,notebook paper, notepad paper, typewriter paper, newspapers, magazines,cardboard and paper-based packaging materials.

The saccharified biomass can be made into a number of bio-basedproducts, via processes such as, e.g., microbial fermentation and/orchemical synthesis. As used herein, “microbial fermentation” refers to aprocess of growing and harvesting fermenting microorganisms undersuitable conditions. The fermenting microorganism can be anymicroorganism suitable for use in a desired fermentation process for theproduction of bio-based products. Suitable fermenting microorganismsinclude, without limitation, filamentous fungi, yeast, and bacteria. Thesaccharified biomass can, e.g., be made it into a fuel (e.g., a biofuelsuch as a bioethanol, biobutanol, biomethanol, a biopropanol, abiodiesel, a jet fuel, or the like) via fermentation and/or chemicalsynthesis. The saccharified biomass can, e.g., also be made into acommodity chemical (e.g., ascorbic acid, isoprene, 1,3-propanediol),lipids, amino acids, proteins, and enzymes, via fermentation and/orchemical synthesis.

Biomass material may include cellulose, hemicellulose, or a mixturethereof. For example, a biomass material may include glucan and/orxylan.

In some aspects, there are provided methods of reducing the viscosity ofa biomass mixture comprising contacting the biomass mixture withnon-naturally occurring composition comprising a polypeptide havingGH61/endoglucanase activity. The polypeptide is in an amount sufficientto reduce the viscosity. The biomass mixture may comprise biomassmaterial (e.g., pretreated biomass material). The biomass mixture maycomprise an enzyme composition such as any of the enzyme compositionsprovided herein or a mixture thereof.

In some aspects, any of the polypeptides, compositions provided hereinmay be used to hydrolyze substrate such as a biomass material or reducethe viscosity of a substrate-enzyme mixture during saccharificationprocess. The substrate may be a biomass material. The substrate may beisolated cellulose or isolated hemicellulose. The substrate may beglucan and/or xylan. In some aspects, the biomass material is pretreatedbiomass material.

Pretreatment of Biomass Material

Prior to saccharification, a biomass material is preferably subject toone or more pretreatment step(s) in order to render xylan,hemicellulose, cellulose and/or lignin material more accessible orsusceptable to enzymes and thus more amenable to hydrolysis by theenzyme(s) and/or enzyme blends/compositions of the disclosure.

Pretreatment may include chemical, physical, and biologicalpretreatment. For example, physical pretreatment techniques can includewithout limitation various types of milling, crushing, steaming/steamexplosion, irradiation and hydrothermolysis. Chemical pretreatmenttechniques can include without limitation dilute acid, alkaline, organicsolvent, ammonia, sulfur dioxide, carbon dioxide, and pH-controlledhydrothermolysis. Biological pretreatment techniques can include withoutlimitation applying lignin-solubilizing microorganisms. The pretreatmentcan occur from several minutes to several hours, such as from about 1hour to about 120.

In some aspects, any of the methods or processes provided herein mayfurther comprise pretreating the biomass material, such as pretreatingthe biomass with acid or base. The acid or base may be ammonia, sodiumhydroxide, or phosphoric acid. The method may further comprisepretreating the biomass material with ammonia. The pretreatment may besteam explosion, pulping, grinding, acid hydrolysis, or combinationsthereof.

In one embodiment, the pretreatment may be by elevated temperature andthe addition of either of dilute acid, concentrated acid or dilutealkali solution. The pretreatment solution can added for a timesufficient to at least partially hydrolyze the hemicellulose componentsand then neutralized

In an exemplary embodiment, the pretreatment entails subjecting biomassmaterial to a catalyst comprising a dilute solution of a strong acid anda metal salt in a reactor. The biomass material can, e.g., be a rawmaterial or a dried material. This pretreatment can lower the activationenergy, or the temperature, of cellulose hydrolysis, ultimately allowinghigher yields of fermentable sugars. See, e.g., U.S. Pat. Nos.6,660,506; 6,423,145.

Another exemplary pretreatment method entails hydrolyzing biomass bysubjecting the biomass material to a first hydrolysis step in an aqueousmedium at a temperature and a pressure chosen to effectuate primarilydepolymerization of hemicellulose without achieving significantdepolymerization of cellulose into glucose. This step yields a slurry inwhich the liquid aqueous phase contains dissolved monosaccharidesresulting from depolymerization of hemicellulose, and a solid phasecontaining cellulose and lignin. The slurry is then subject to a secondhydrolysis step under conditions that allow a major portion of thecellulose to be depolymerized, yielding a liquid aqueous phasecontaining dissolved/soluble depolymerization products of cellulose.See, e.g., U.S. Pat. No. 5,536,325.

A further example of method involves processing a biomass material byone or more stages of dilute acid hydrolysis using about 0.4% to about2% of a strong acid; followed by treating the unreacted solidlignocellulosic component of the acid hydrolyzed material with alkalinedelignification. See, e.g., U.S. Pat. No. 6,409,841.

Another example of pretreatment method comprises prehydrolyzing biomass(e.g., lignocellulosic materials) in a prehydrolysis reactor; adding anacidic liquid to the solid lignocellulosic material to make a mixture;heating the mixture to reaction temperature; maintaining reactiontemperature for a period of time sufficient to fractionate thelingo-cellulosic material into a solubilized portion containing at leastabout 20% of the lignin from the lignocellulosic material, and a solidfraction containing cellulose; separating the solubilized portion fromthe solid fraction, and removing the solubilized portion while at ornear reaction temperature; and recovering the solubilized portion. Thecellulose in the solid fraction is rendered more amenable to enzymaticdigestion. See, e.g., U.S. Pat. No. 5,705,369.

Further pretreatment methods can involve the use of hydrogen peroxideH₂O₂. See Gould, 1984, Biotech, and Bioengr. 26:46-52.

Pretreatment can also comprise contacting a biomass material withstoichiometric amounts of sodium hydroxide and ammonium hydroxide at avery low concentration. See Teixeira et al., 1999, Appl. Biochem. andBiotech. 77-79:19-34. Pretreatment can also comprise contacting alignocellulose with a chemical (e.g., a base, such as sodium carbonateor potassium hydroxide) at a pH of about 9 to about 14 at moderatetemperature, pressure, and pH. See PCT Publication WO2004/081185.

Ammonia may be used in a pretreatment method. Such a pretreatment methodcomprises subjecting a biomass material to low ammonia concentrationunder conditions of high solids. See, e.g., U.S. Patent Publication20070031918, PCT publication WO 06110901.

Saccharification Process and Viscosity Reduction

The present disclosure provides methods of reducing the viscosity of abiomass mixture comprising contacting the biomass mixture with acomposition (e.g., a non-naturally occurring composition) comprising apolypeptide having glycosyl hydrolase family 61 (“GH61”) endoglucanaseactivity in an amount sufficient to reduce the viscosity of the biomassmixture. In some aspects, the biomass mixture comprises a biomassmaterial, fermentable sugar(s), whole cellulase, a compositioncomprising a polypeptide having cellulase activity, and/or a polypeptidehaving hemicellulase activity. In some aspects, the viscosity is reducedby at least about 5%, (e.g., at least about any of 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, or 90%) compared to theviscosity of a biomass mixture in the absence of a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof).In some aspects of any of the methods described herein, the biomassmaterial comprises hemicellulose, cellulose, or a mixture thereof. Insome aspects, the biomass material comprises glucan, xylan and/orlignin.

The methods and processes provided herein may be performed under variousconditions. For example, any of the methods provided herein may beperformed at a pH in the range of pH of about 3.5 to about 7.0, forexample, pH of about 4.0 to about 6.5, pH of about 4.4 to about 6.0, pHof about 4.8 to about 5.6, or about 4.5 to about 5.5. Thesaccharification mixture containing biomass material may be adjusted tothe desired pH using base or acid (such as sulfuric acid) according toany of the methods known to one of ordinary skill in the art. Forexample, the pretreated biomass material may be added with base or acid(such as sulfuric acid) to achieve the desired pH for saccharification.Any of the methods for hydrolyzing a biomass material or reducing theviscosity of the biomass mixture may be conducted at a pH of about 4.8to about 5.6 (e.g., pH of about any of 4.8, 4.9, 5.0, 5.1, 5.2, 5.3,5.4, 5.5, or 5.6). In some aspects, the method further comprisesadjusting the pH of the biomass mixture to a pH of about 4.0 to about6.5 (e.g., pH of about 4.5 to about 5.5).

The methods and processes provided herein may be performed for anylength of time, e.g., 1 hour, 2 hours, 4 hours, 8 hours, 12 hours, 18hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days,10 days, 14 days, 3 weeks, or 4 weeks. After any of the saccharificationtime described herein, the amount of fermentable sugar(s) is increasedand/or the viscosity of the saccharification mixture is reduced. In someaspects, the method is performed for about 2 hours to about 7 days(e.g., about 4 hours to about 6 days, about 8 hours to about 5 days, orabout 8 hours to about 3 days).

A composition (e.g., a non-naturally occurring composition) comprisingpolypeptide having GH61/endoglucanase activity (e.g., EG IV such as T.reesei Eg4 or a variant thereof) may be added after the biomass materialis pretreated. A composition (e.g., a non-naturally occurringcomposition) comprising polypeptide having GH61/endoglucanase activity(e.g., EG IV such as T. reesei Eg4 or a variant thereof) may be added tothe biomass material before or after another enzyme composition (such asan enzyme composition comprising hemicellulose, cellulase, or wholecellulase) is added to the biomass material. A composition (e.g., anon-naturally occurring composition) comprising polypeptide havingGH61/endoglucanase activity (e.g., EG IV such as T. reesei Eg4 or avariant thereof) may be added to the biomass mixture containing (a)biomass material and/or fermentable sugars and (b) enzyme (such ashemicellulase or cellulase including whole cellulase). In some aspects,a composition (e.g., a non-naturally occurring composition) comprisingpolypeptide having GH61/endoglucanase activity (e.g., EG IV such as T.reesei Eg4 or a variant thereof) is added to the biomass mixture,wherein the biomass material has been hydrolyzed for a period of time(such as about any of 5 minutes, 10 minutes, 30 minutes, 1 hour, 2hours, 4 hours, 8 hours, 12 hours, 18 hours, 24 hours, 2 days, 3 days, 4days, or 5 days).

A composition (e.g., a non-naturally occurring composition) comprisingisolated polypeptide having GH61/endoglucanase activity (e.g., EG IVsuch as T. reesei Eg4 or a variant thereof) may be added to biomassmaterial during saccharification. A composition (e.g., a non-naturallyoccurring composition) comprising whole cellulase may be added tobiomass material during saccharification, where the whole cellulasecomprises a polypeptide having GH61/endoglucanase activity (e.g., EG IVsuch as T. reesei Eg4 or a variant thereof).

A biomass material used in any one of the methods may be in liquid form,solid form, or a mixture thereof. A biomass material used in any one ofthe methods may be wet form, dry form, a material having various degreeof moisture, or a mixture thereof. A biomass material used in any one ofthe methods may be in a dry solid form (such as a dry solid form as astarting material). The biomass material may be processed into any ofthe following forms: wet form, dry form, solid form, liquid form, or amixture thereof according to any method known to one skilled in the art.

A biomass material used in any of the methods may be present in thesaccharification mixture in an amount of at least about any of 0.5 wt.%, 1 wt. %, 5 wt. %, 10 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %,35 wt. %, 40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, or 60 wt. % of totalweight of hydrolysis mixture or saccharification mixture, wherein theamount of the biomass material refers to the weight amount of thebiomass material in its solid state (or the biomass material in its drystate, its dry solid state, its natural state, or its unprocessedstate). The biomass material may also be in an amount of about 0.5 wt. %to about 55 wt. %, 1 wt. % to about 40 wt. %, 5 wt. % to about 60 wt. %,about 10 wt. % to about 55 wt. %, about 10 wt. % to about 50 wt. %,about 15 wt. % to about 50 wt. %, about 15 wt. % to about 40 wt. %,about 15 wt. % to about 35 wt. %, about 15 wt. % to about 30 wt. %,about 20 wt. % to about 35 wt. %, or about 20 wt. % to about 30 wt. % ofa hydrolyzing mixture containing biomass material, wherein the amount ofthe biomass material refers to the weight amount of the biomass materialin its solid state (or the biomass material in its dry state, its drysolid state, its natural state, or its unprocessed state). A biomassmaterial used in any of the methods may be present in thesaccharification mixture in an amount of about any of 0.5 wt. %, 1 wt.%. 5 wt. %, 10 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 35 wt. %,40 wt. %, 45 wt. %, 50 wt. %, 55 wt. %, or 60 wt. % of total weight ofhydrolysis mixture or saccharification mixture, wherein the amount ofthe biomass material refers to the weight amount of the biomass materialin its solid state (or the biomass material in its dry state, its drysolid state, its natural state, or its unprocessed state).

The hydrolysis mixture or saccharification mixture includes biomassmaterial, enzyme(s) (e.g., any one of polypeptides provided herein),enzyme composition (e.g., any one of the compositions provided herein),and/or other components such as components necessary forsaccharification.

Any of the compositions provided herein may be used in the methodsdescribed herein such as any one of the compositions provided above inthe “Exemplary compositions” section. The amount of any of thecompositions described herein used in any one of the methods providedherein may be in the range of about 0.05 mg to about 50 mg, about 0.1 mgto about 40 mg, about 0.2 mg to about 30 mg, about 0.5 mg to about 25mg, about 1 mg to about 25 mg, about 2 mg to about 25 mg, about 5 mg toabout 25 mg, or about 10 mg to about 25 mg protein per gram ofcellulose, hemicellulose, or a mixture of cellulose and hemicellulosecontained in the biomass material. A non-naturally occurring compositioncomprising a polypeptide having GH61/endoglucanase activity (e.g., EG IVsuch as T. reesei Eg4 or a variant thereof) used in any one of themethods for hydrolyzing a biomass material and/or methods for reducingthe viscosity of the biomass mixture may be in an amount of about 0.05mg to about 50 mg, about 0.1 mg to about 40 mg, about 0.2 mg to about 30mg, about 0.5 mg to about 25 mg, about 1 mg to about 25 mg, about 2 mgto about 25 mg, about 5 mg to about 25 mg, or about 10 mg to about 25 mgprotein per gram of cellulose, hemicellulose, or a mixture of celluloseand hemicellulose contained in the substrate such as biomass material.

In some aspects, a non-naturally occurring composition comprising apolypeptide having GH61/endoglucanase activity (e.g., EG IV such as T.reesei Eg4 or a variant thereof) used in any of the methods forhydrolyzing a biomass material and/or methods for reducing the viscosityof the biomass mixture is in an amount of at least about any of 0.05 mg,0.1 mg, 0.2 mg, 0.5 mg, 1 mg, 2 mg, 5 mg, 7.5 mg, 10 mg, 12 mg, 14 mg,15 mg, 16 mg, 17.5 mg, 18 mg, 20 mg, 22.5 mg, 25 mg, 27.g mg, 30 mg, 35mg, 40 mg, 45 mg, or 50 mg protein per gram of cellulose, hemicellulose,or a mixture of cellulose and hemicellulose contained in the substratesuch as biomass material. In some aspects, a non-naturally occurringcomposition comprising a polypeptide having GH61/endoglucanase activity(e.g., EG IV such as T. reesei Eg4 or a variant thereof) used in any ofthe methods for hydrolyzing a biomass material and/or methods forreducing the viscosity of the biomass mixture is in an amount of no morethan about any of 0.1 mg, 0.2 mg, 0.5 mg, 1 mg, 2 mg, 5 mg, 7.5 mg, 10mg, 12 mg, 14 mg, 15 mg, 16 mg, 17.5 mg, 18 mg, 20 mg, 22.5 mg, 25 mg,27.5 g mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 55 mg, 60 mg, 65 mg, 75mg, or 100 mg protein per gram of cellulose, hemicellulose, or a mixtureof cellulose and hemicellulose contained in the substrate such asbiomass material. In some aspects, a non-naturally occurring compositioncomprising a polypeptide having GH61/endoglucanase activity (e.g., EG IVsuch as T. reesei Eg4 or a variant thereof) used in any of the methodsfor hydrolyzing a biomass material and/or methods for reducing theviscosity of the biomass mixture is in an amount of about any of 0.05mg, 0.1 mg, 0.2 mg, 0.5 mg, 1 mg, 2 mg, 5 mg, 7.5 mg, 10 mg, 12 mg, 14mg, 15 mg, 16 mg, 17.5 mg, 18 mg, 20 mg, 22.5 mg, 25 mg, 27.5 g mg, 30mg, 35 mg, 40 mg, 45 mg, or 50 mg protein per gram of cellulose,hemicellulose, or a mixture of cellulose and hemicellulose contained inthe substrate such as biomass material. The amount of cellulose,hemicellulose, or a mixture of cellulose and hemicellulose contained inthe substrate such as biomass material may be calculated using anymethods known to one skilled in the art. The biomass material maycomprise glucan, xylan, and/or lignin.

In some aspects of any of the methods described herein, the amount ofthe composition comprising a polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof) is about 0.1 mg toabout 50 mg protein (e.g., about 0.2 mg to about 40 mg protein, about0.5 mg to about 30 mg protein, about 1 mg to about 20 mg protein, orabout 5 mg to about 15 mg protein) per gram of cellulose, hemicellulose,or a mixture of cellulose and hemicellulose contained in the biomassmaterial. The protein amount described herein refers to the weight oftotal protein in the composition. The proteins include a polypeptidehaving GH61/endoglucanase activity (e.g., T. reesei Eg4 or a variantthereof) and may also include other enzymes such as cellulasepolypeptide(s) and/or hemicellulase polypeptide(s) in the composition.

In some aspects of any of the methods described herein, the amount ofthe polypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4or a variant thereof) is about 0.2 mg to about 30 mg (e.g., about 0.2 mgto about 20 mg protein, about 0.5 mg to about 10 mg protein, or about 1mg to about 5 mg protein) per gram of cellulose, hemicellulose, or amixture of cellulose and hemicellulose contained in the biomassmaterial.

In some aspects of any of the methods described herein, the compositioncomprises a polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof) and at least one polypeptide havingendoglucanase activity (e.g., T. reesei Eg1, T. reesei Eg2, and/or avariant thereof), wherein the total amount of the polypeptides havingendoglucanase activity is about 0.2 mg to about 30 mg (e.g., about 0.2mg to about 20 mg protein, about 0.5 mg to about 10 mg protein, or about1 mg to about 5 mg protein) per gram of cellulose, hemicellulose, or amixture of cellulose and hemicellulose contained in the biomassmaterial.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one polypeptide having cellobiohydrolase activity (e.g., T.reesei CBH1, T. reesei CBH2, and/or a variant thereof), wherein theamount of the polypeptide(s) having cellobiohydrolase activity is about0.2 mg to about 30 mg (e.g., about 0.2 mg to about 20 mg protein, about0.5 mg to about 10 mg protein, or about 1 mg to about 5 mg protein) pergram of cellulose, hemicellulose, or a mixture of cellulose andhemicellulose contained in the biomass material.

In some aspects of any of the methods described herein, the compositioncomprises a polypeptide having GH61/endoglucanase activity (e.g., T.reesei Eg4 or a variant thereof) and at least one polypeptide havingβ-glucosidase activity (e.g., an Fv3C, a Pa3D, an Fv3G, an Fv3D, a Tr3A,a Tr3B, a Te3A, an An3A, an Fo3A, a Gz3A, an Nh3A, a Vd3A, a Pa3G, aTn3B, or a variant thereof), wherein the amount of the polypeptide(s)having β-glucosidase activity is about 0.2 mg to about 30 mg (e.g.,about 0.2 mg to about 20 mg protein, about 0.5 mg to about 10 mgprotein, or about 0.5 mg to about 5 mg protein) per gram of cellulose,hemicellulose, or a mixture of cellulose and hemicellulose contained inthe biomass material.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one polypeptide having xylanase activity (e.g., T. reeseiXyn3, T. reesei Xyn2, an AfuXyn2, an AfuXyn5, or a variant thereof),wherein the amount of the polypeptide(s) having xylanase activity isabout 0.2 mg to about 30 mg (e.g., about 0.2 mg to about 20 mg protein,about 0.5 mg to about 10 mg protein, or about 0.5 mg to about 5 mgprotein) per gram of cellulose, hemicellulose, or a mixture of celluloseand hemicellulose contained in the biomass material.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one polypeptide having β-xylosidase activity (e.g., Fv3A,Fv43A, a Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, aPa51A, a Gz43A, a T. reesei Bxl1, or a variant thereof), wherein theamount of the polypeptide(s) having β-xylosidase activity is about 0.2mg to about 30 mg (e.g., about 0.2 mg to about 20 mg protein, about 0.5mg to about 10 mg protein, or about 0.5 mg to about 5 mg protein) pergram of cellulose, hemicellulose, or a mixture of cellulose andhemicellulose contained in the biomass material.

In some aspects, the composition comprises a polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one polypeptide having L-α-arabinofuranosidase activity(e.g., an Af43A, an Fv43B, a Pf51A, a Pa51A, an Fv51A, or a variantthereof), wherein the amount of the polypeptide(s) havingL-α-arabinofuranosidase activity is about 0.2 mg to about 30 mg (e.g.,about 0.2 mg to about 20 mg protein, about 0.5 mg to about 10 mgprotein, or about 0.5 mg to about 5 mg protein) per gram of cellulose,hemicellulose, or a mixture of cellulose and hemicellulose contained inthe biomass material.

In any one of the methods provided herein, the viscosity of the biomassmixture may be reduced by at least about any of 5%, 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%compared to the viscosity of the biomass mixture in the absence of anenzyme composition provided herein. For example, there are providedmethods of reducing the viscosity of a biomass mixture comprisingcontacting the biomass mixture with a non-naturally occurringcomposition comprising a polypeptide having GH61/endoglucanase activity(e.g., EG IV such as T. reesei Eg4 or a variant thereof), wherein theviscosity is reduced by at least about any of 5%, 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%compared to the viscosity of the biomass mixture in the absence of apolypeptide having GH61/endoglucanase activity (e.g., EG IV such as T.reesei Eg4 or a variant thereof). In some aspects, the viscosity isreduced by about any of 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% compared to the viscosityof the biomass mixture in the absence of a polypeptide havingGH61/endoglucanase activity (e.g., EG IV such as T. reesei Eg4 or avariant thereof). The reduction of viscosity described herein is seenafter a certain period of saccharification. For example, the reductionof viscosity is seen after 30 minutes, 1 hour, 2 hours, 4 hours, 8hours, 12 hours, 18 hours, 24 hours, 2 days, 3 days, 4 days, or 5 dayssaccharification. Methods of measuring viscosity are known in the art.For example, viscosity may be measured by human eyes, or be measured bya viscometer such as Brookfield viscometer (Brookfield Engineering,Inc). For example, viscosity of saccharification reaction mixture can bemeasured using a viscosity meter with ammonia-pretreated corncob assubstrates. A viscosity meter can measure the resistance (torque) ittakes to turn a spindle at a constant rate in the slurry.

The methods provided herein may be conducted at a temperature that issuitable for saccharification. For example, any one of the methodsdescribed herein may be performed at about 20° C. to about 75° C., about25° C. to about 70° C., about 30° C. to about 65° C., about 35° C. toabout 60° C., about 37° C. to about 60° C., about 40° C. to about 60°C., about 40° C. to about 55° C., about 40° C. to about 50° C., or about45° C. to about 50° C. In some aspects, any one of the methods describedherein may be performed at about 20° C., about 25° C., about 30° C.,about 35° C., about 37° C., about 40° C., about 45° C., about 48° C.,about 50° C., about 55° C., about 60° C., about 65° C., about 70° C., orabout 75° C.

In some aspects of any of the methods described herein, the methodcomprises producing fermentable sugar(s), wherein the amount of thefermentable sugar(s) is increased by at least about 5% (e.g., at leastabout any of 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%,80%, or 90%) compared to the amount of the fermentable sugar(s) producedin the absence of a polypeptide having GH61/endoglucanase activity(e.g., T. reesei Eg4 or a variant thereof).

Also provided herein are methods of increasing the amount of fermentablesugar(s) (and/or increasing the conversion from a biomass material tofermentable sugar(s) such as glucan conversion) by using a composition(e.g., a non-naturally occurring composition) comprising a polypeptidehaving GH61/endoglucanase activity (e.g., EG IV such as T. reesei Eg4 ora variant thereof) during hydrolysis of biomass material. There arevarious fermentable sugars produced from hydrolysis of biomass material,including but are not limited to, glucose, xylose, and/or cellobiose. Insome aspects, the amount of fermentable sugar(s) produced fromhydrolysis of biomass material may be increased by at least about any of5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, or 95% compared to the amount of fermentablesugar(s) in the absence of an enzyme composition provided herein. Forexample, there are provided methods of increasing the amount offermentable sugar(s) comprising contacting the biomass material with anon-naturally occurring composition comprising a polypeptide havingGH61/endoglucanase activity (e.g., EG IV such as T. reesei Eg4 or avariant thereof) (to start or further a saccharification process),wherein the amount of fermentable sugar(s) from saccharification isincreased by at least about any of 5%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% comparedto the amount of fermentable sugar(s) from saccharification in theabsence of a polypeptide having GH61/endoglucanase activity (e.g., EG IVsuch as T. reesei Eg4 or a variant thereof). In some aspects, the amountof fermentable sugar(s) from saccharification is increased by about anyof 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, or 95% compared to the amount of fermentablesugar(s) from saccharification in the absence of a polypeptide havingGH61/endoglucanase activity (e.g., EG IV such as T. reesei Eg4 or avariant thereof). The increase in amount of fermentable sugar(s)produced from hydrolysis of biomass material described herein is seenafter a certain period of saccharification. For example, the increase inamount of fermentable sugar(s) is seen after 30 minutes, 1 hour, 2hours, 4 hours, 8 hours, 12 hours, 18 hours, 24 hours, 2 days, 3 days, 4days, or 5 days saccharification. Methods of measuring amount offermentable sugar(s) and/or glucan conversion are known to a personskilled in the art.

The reduction in viscosity of saccharification mixture may correlatewith improved yield of desirable fermentable sugars.

In some aspects, the method further comprises the step of contacting thebiomass material with a composition comprising whole cellulase. In someaspects, the step of further contacting the biomass material with acomposition comprising whole cellulase is performed before, after, orconcurrently with contacting the biomass material with compositioncomprising a polypeptide having glycosyl hydrolase family 61 (“GH61”)endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof).

In some aspects of any of the methods described herein, the methodcomprises the step of further contacting the biomass material with acomposition comprising a polypeptide having cellulase activity and/or apolypeptide having hemicellulase activity. In some aspects, the step offurther contacting the biomass material with a composition comprising apolypeptide having cellulase activity and/or a polypeptide havinghemicellulase activity is performed before, after, or concurrently withcontacting the biomass material with composition comprising apolypeptide having glycosyl hydrolase family 61 (“GH61”) endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof).

In some aspects, the composition comprises the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and further comprises at least one cellulase polypeptide and/or at leastone hemicellulase polypeptide, wherein the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one cellulase polypeptide and/or at least one hemicellulasepolypeptide are mixed together before contacting the biomass materialwith a composition comprising the polypeptide having GH61/endoglucanaseactivity (e.g., T. reesei Eg4 or a variant thereof).

In some aspects, the composition comprises the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and further comprises at least one cellulase polypeptide and/or at leastone hemicellulase polypeptide, wherein the polypeptide havingGH61/endoglucanase activity (e.g., T. reesei Eg4 or a variant thereof)and at least one cellulase polypeptide and/or at least one hemicellulasepolypeptide are added to the biomass material at different times (e.g.,the polypeptide having GH61/endoglucanase activity (e.g., T. reesei Eg4or a variant thereof) is added before or after at least one cellulasepolypeptide and/or at least one hemicellulase polypeptide is added tothe biomass material).

Enhanced cellulose conversion may be achieved at higher temperaturesusing the CBH polypeptides described in, for example, any one of thefollowing US Patent Publications US20050054039, US20050037459,US20060205042, US20050048619A1 and US20060218671. Methods ofoverexpressing β-glucosidase are known in the art. See, e.g., U.S. Pat.No. 6,022,725. See also, e.g., US Patent Publication 20050214920.

The methods of the present disclosure can be used in the production ofmonosaccharides, disaccharides, and polysaccharides as chemical,fermentation feedstocks for microorganism, and inducers for theproduction of proteins, organic products, chemicals and fuels, plastics,and other products or intermediates. In particular, the value ofprocessing residues (dried distillers grain, spent grains from brewing,sugarcane bagasse, etc.) can be increased by partial or completesolubilization of cellulose or hemicellulose. In addition to ethanol,chemicals that can be produced from cellulose and hemicellulose include,acetone, acetate, glycine, lysine, organic acids (e.g., lactic acid),1,3-propanediol, butanediol, glycerol, ethylene glycol, furfural,polyhydroxyalkanoates, cis, cis-muconic acid, animal feed and xylose.

Business Methods

The cellulase and/or hemicellulase compositions of the disclosure can befurther used in industrial and/or commercial settings. Accordingly amethod or a method of manufacturing, marketing, or otherwisecommercializing the instant non-naturally occurring cellulase and/orhemicellulase compositions is also contemplated.

In a specific embodiment, the non-naturally occurring cellulase and/orhemicellulase compositions of the invention, for example, comprising oneor more of the GH61 endoglucanases or variants thereof as describedherein, can be supplied or sold to certain ethanol (bioethanol)refineries or other bio-chemical or bio-material manufacturers. In afirst example, the non-naturally occurring cellulase and/orhemicellulase compositions can be manufactured in an enzymemanufacturing facility that is specialized in manufacturing enzymes atan industrial scale. The non-naturally occurring cellulase and/orhemicellulase compositions can then be packaged or sold to customers ofthe enzyme manufacturer. This operational strategy is termed the“merchant enzyme supply model” herein.

In another operational strategy, the non-naturally occurring cellulaseand hemicellulase compositions of the invention can be produced in astate of the art enzyme production system that is built by the enzymemanufacturer at a site that is located at or in the vicinity of thebioethanol refineries or the bio-chemical/biomaterial manufacturers(“on-site”). In some embodiments, an enzyme supply agreement is executedby the enzyme manufacturer and the bioethanol refinery or thebio-chemical/biomaterial manufacturer. The enzyme manufacturer designs,controls and operates the enzyme production system on site, utilizingthe host cell, expression, and production methods as described herein toproduce the non-naturally-occurring cellulase and/or hemicellulasecompositions. In certain embodiments, suitable biomass, preferablysubject to appropriate pretreatments as described herein, can behydrolyzed using the saccharification methods and the enzymes and/orenzyme compositions herein at or near the bioethanol refineries or thebio-chemical/biomaterial manufacturing facilities. The resultingfermentable sugars can then be subject to fermentation at the samefacilities or at facilities in the vicinity. This operational strategyis termed the “on-site biorefinery model” herein.

The on-site biorefinery model provides certain advantages over themerchant enzyme supply model, including, e.g., the provision of aself-sufficient operation, allowing minimal reliance on enzyme supplyfrom merchant enzyme suppliers. This in turn allows the bioethanolrefineries or the bio-chemical/biomaterial manufacturers to bettercontrol enzyme supply based on real-time or nearly real-time demand. Incertain embodiments, it is contemplated that an on-site enzymeproduction facility can be shared between two or among two or morebioethanol refineries and/or the bio-chemical/biomaterial manufacturerswho are located near to each other, reducing the cost of transportingand storing enzymes. Moreover, this allows more immediate “drop-in”technology improvements at the enzyme production facility on-site,reducing the time lag between the improvements of enzyme compositions toa higher yield of fermentable sugars and ultimately, bioethanol orbiochemicals.

The on-site biorefinery model has more general applicability in theindustrial production and commercialization of bioethanols andbiochemicals, in that it can be used to manufacture, supply, and producenot only the cellulase and non-naturally occurring hemicellulasecompositions of the present disclosure but also those enzymes and enzymecompositions that process starch (e.g., corn) to allow for moreefficient and effective direct conversion of starch to bioethanol orbio-chemicals. The starch-processing enzymes can, in certainembodiments, be produced in the on-site biorefinery, then quickly andeasily integrated into the bioethanol refinery or thebiochemical/biomaterial manufacturing facility in order to producebioethanol.

Thus in certain aspects, the invention also pertains to certain businessmethod of applying the enzymes (e.g., certain GH61 endoglucanases andvariants thereof), cells, compositions (e.g., comprising a suitable GH61endoglucanase or a variant thereof), and processes herein in themanufacturing and marketing of certain bioethanol, biofuel, biochemicalsor other biomaterials. In some embodiments, the invention pertains tothe application of such enzymes, cells, compositions and processes in anon-site biorefinery model. In other embodiments, the invention pertainsto the application of such enzymes, cells, compositions and processes ina merchant enzyme supply model.

Relatedly, the disclosure provides the use of the enzymes and/or theenzyme compositions of the invention in a commercial setting. Forexample, the enzymes and/or enzyme compositions of the disclosure can besold in a suitable market place together with instructions for typicalor preferred methods of using the enzymes and/or compositions.Accordingly the enzymes and/or enzyme compositions of the disclosure canbe used or commercialized within a merchant enzyme supplier model, wherethe enzymes and/or enzyme compositions of the disclosure are sold to amanufacturer of bioethanol, a fuel refinery, or a biochemical orbiomaterials manufacturer in the business of producing fuels orbio-products. In some aspects, the enzyme and/or enzyme composition ofthe disclosure can be marketed or commercialized using an on-sitebio-refinery model, wherein the enzyme and/or enzyme composition isproduced or prepared in a facility at or near to a fuel refinery orbiochemical/biomaterial manufacturer's facility, and the enzyme and/orenzyme composition of the invention is tailored to the specific needs ofthe fuel refinery or biochemical/biomaterial manufacturer on a real-timebasis. Moreover, the disclosure relates to providing these manufacturerswith technical support and/or instructions for using the enzymes and. orenzyme compositions such that the desired bio-product (e.g., biofuel,bio-chemicals, bio-materials, etc) can be manufactured and marketed.

The following are examples of the methods and compositions of theinvention. It is understood that various other embodiments may bepracticed, given the general description provided above.

EXAMPLES Example 1 Assays/Methods

The following assays/methods were generally used in the Examplesdescribed below. Any deviations from the protocols provided below areindicated in specific Examples.

A. Pretreatment of Biomass Substrates

Corncob, corn stover and switch grass were pretreated prior to enzymatichydrolysis according to the methods and processing ranges described inInternational Patent Publication WO06110901A (unless otherwise noted).These references for pretreatment are also included in the disclosuresof US Patent Application Publications 20070031918-A1, 20070031919-A1,20070031953-A1, and/or 20070037259-A1.

Ammonia fiber explosion treated (AFEX) corn stover was obtained fromMichigan Biotechnology Institute International (MBI). The composition ofthe corn stover was determined by MBI (Teymouri, F et al. AppliedBiochemistry and Biotechnology, 2004, 113:951-963) using the NationalRenewable Energy Laboratory (NREL) procedure, NREL LAP-002. NRELprocedures are available at:http://www.nrel.gov/biomass/analytical_procedures.html.

The FPP pulp and paper substrates were obtained from SMURFIT KAPPACELLULOSE DU PIN, France.

Steam Expanded Sugar-cane Bagasse (SEB) was obtained from SunOpta(Glasser, W G et al. Biomass and Bioenergy 1998, 14(3): 219-235; Jollez,P et al. Advances in thermochemical biomass conversion, 1994,2:1659-1669).

B. Compositional Analysis of Biomass

The 2-step acid hydrolysis method described in Determination ofstructural carbohydrates and lignin in the biomass (National RenewableEnergy Laboratory, Golden, Colo. 2008http://www.nrel.gov/biomass/pdfs/42618.pdf) was used to measure thecomposition of biomass substrates. Using this method, enzymatichydrolysis results were reported herein in terms of percent conversionwith respect to the theoretical yield from the starting glucan and xylancontent of the substrate.

C. Total Protein Assay

The BCA protein assay is a colorimetric assay that measures proteinconcentration with a spectrophotometer. The BCA Protein Assay Kit(Pierce Chemical, Product #23227) was used according to themanufacturer's suggestion. Enzyme dilutions were prepared in test tubesusing 50 mM sodium acetate pH 5 buffer. Diluted enzyme solution (0.1 mL)was added to 2 mL Eppendorf centrifuge tubes containing 1 mL 15%tricholoroacetic acid (TCA). The tubes were vortexed and placed in anice bath for 10 min. The samples were then centrifuged at 14,000 rpm for6 min. The supernatant was poured out, the pellet was resuspended in 1mL 0.1 N NaOH, and the tubes vortexed until the pellet dissolved. BSAstandard solutions were prepared from a stock solution of 2 mg/mL. BCAworking solution was prepared by mixing 0.5 mL Reagent B with 25 mLReagent A. 0.1 mL of the enzyme resuspended sample was added to 3Eppendorf centrifuge tubes. Two (2) mL Pierce BCA working solution wasadded to each sample and BSA standard Eppendorf tubes. All tubes wereincubated in a 37° C. waterbath for 30 min. The samples were then cooledto room temperature (15 min) and the absorbance measured at 562 nm in aspectrophotometer.

Average values for the protein absorbance for each standard werecalculated. The average protein standard was plotted, absorbance onx-axis and concentration (mg/mL) on the y-axis. The points were fit to alinear equation:

y=mx+b

The raw concentration of the enzyme samples was calculated bysubstituting the absorbance for the x-value. The total proteinconcentration was calculated by multiplying with the dilution factor.

The total protein of purified samples was determined by A280 (Pace, C N,et al. Protein Science, 1995, 4:2411-2423).

The total protein content of fermentation products was sometimesmeasured as total nitrogen by combustion, capture and measurement ofreleased nitrogen, either by Kjeldahl (rtech laboratories,www.rtechlabs.com) or in-house by the DUMAS method (TruSpec CN,www.leco.com) (Sader, A. P. O. et al., Archives of Veterinary Science,2004, 9(2):73-79). For complex protein-containing samples, e.g.fermentation broths, an average 16% N content, and the conversion factorof 6.25 for nitrogen to protein was used. In some cases, totalprecipitable protein was measured to remove interfering non-proteinnitrogen. A 12.5% final TCA concentration was used and theprotein-containing TCA pellet was resuspended in 0.1 M NaOH.

In some cases, Coomassie Plus—the Better Bradford Assay (ThermoScientific, Rockford, Ill. product #23238) was used according tomanufacturer recommendation. In other cases, total protein was measuredusing the Biuret method as modified by Weichselbaum and Gornall usingBovine Serum Albumin as a calibrator (Weichselbaum, T. Amer. J. Clin.Path. 1960, 16:40; Gornall, A. et al. J. Biol. Chem. 1949, 177:752).

D. Glucose Determination Using ABTS

The ABTS (2,2′-azino-bis(3-ethylenethiazoline-6)-sulfonic acid) assayfor glucose determination is based on the principle that in the presenceof O₂, glucose oxidase catalyzes the oxidation of glucose whileproducing stoichiometric amounts of hydrogen peroxide (H₂O₂). Thisreaction is followed by the horse radish peroxidase (HRP) catalyzedoxidation of ABTS which linearly correlates to the concentration ofH₂O₂. The emergence of oxidized ABTS is indicated by the evolution of agreen color, which is quantified at an OD of 405 nm. A mixture of ABTSpowder (Sigma, #A1888-5g 2.74 mg/mL), 0.1 U/mL HRP (100 U/mL, Sigma,#P8375) and 1 U/mL Glucose Oxidase, (OxyGO® HP L5000, 5000 U/mL,Genencor Division, Danisco USA) was prepared in 50 mM Na Acetate Buffer,pH 5.0 and kept in the dark (substrate). Glucose standards (0, 2, 4, 6,8, 10 nmol) were prepared in 50 mM Na Acetate Buffer, pH 5.0 and 10 μLof each standard was added to a 96-well flat bottom MTP in triplicate.Ten (10) μL of serially diluted samples were also added to the MTP. Onehundred (100) μL of ABTS substrate solution was added to each well andthe plate was placed on a spectrophotometric plate reader to kineticallyread oxidation of ABTS for 5 min at 405 nm.

Alternately absorbance at 405 nm was measured after 15-30 min ofincubation followed by quenching of the reaction with 50 mM Na AcetateBuffer, pH 5.0 containing 2% SDS.

E. Sugar Analysis by HPLC

Samples from biomass saccharification were prepared by centrifugation toclear insoluble material, filtration through a 0.22 μm nylon filter(Spin-X centrifuge tube filter, Corning Incorporated, Corning, N.Y.) anddilution to an appropriate concentration of soluble sugars withdistilled water. Monomer sugars were determined on a Shodex Sugar SH-GSH1011, 8×300 mm with a 6×50 mm SH-1011P guard column (www.shodex.net).Solvent was 0.01 NH₂SO₄ run at 0.6 mL/min. Column temperature was 50° C.and detection was by refractive index. Alternately, sugars were analyzedusing a Biorad Aminex HPX-87H column with a Waters 2410 refractive indexdetector. The analysis time was 20 mM, the injection volume was 20 μL ofdiluted sample, the mobile phase was 0.01 N sulfuric acid, 0.2 μmfiltered and degassed, the flow rate was 0.6 mL/min and the columntemperature was 60° C. External standards of glucose, xylose andarabinose were run with each sample set.

Oligomeric sugars were separated by size exclusion chromatography inHPLC using a Tosoh Biosep G2000PW column 7.5 mm×60 cm(www.tosohbioscience.de). The solvent was distilled water at 0.6 mL/minand the column was run at room temperature. Six carbon sugar standardsused for size calibration were: stachyose, raffinose, cellobiose andglucose; and 5 carbon sugars were: xylohexose, xylopentose, xylotetrose,xylotriose, xylobiose and xylose. Xylo-oligomers were obtained fromMegazyme (www.megazyme.com). Detection was by refractive index and whenreported quantitatively results are either as peak area units orrelative peak areas by percent.

Total soluble sugars were determined by hydrolysis of the centrifugedand filter clarified samples described above. The clarified sample wasdiluted 1 to 1 with 0.8 NH₂SO₄ and the resulting solution was autoclavedin a capped vial for a total cycle time of 1 h at 121° C. Results arereported without correction for loss of monomer sugar during thehydrolysis.

F. Oligomer Preparation from Cob and Enzyme Assays

Oligomers from T. reesei Xyn3 hydrolysis of corncobs were prepared byincubating 8 mg T. reesei Xyn3 per g Glucan+Xylan with 250 g dry weightof dilute ammonia pretreated corncob in 50 mM pH 5.0 Na Acetate buffer(pH adjusted with 1 N sulfuric acid). The reaction proceeded for 72 h at48° C., 180 rpm rotary shaking. The supernatant was centrifuged 9,000×G,then filtered through 0.22 μm Nalgene filters to recover the solublesugars. For subsequent enzyme assays, 100 μL aliquots of the T. reeseiXyn3 oligomer-containing supernatant were incubated with 1 μg/μL ofeither T. reesei integrated strain H3A, 1 μg/mL of T. reesei integratedstrain H3A/EG4#27 or water control in Eppendorf tubes at 48° C. for 2.5h. The supernatants were then diluted 4× with ice cold MilliQ water,filtered, and analyzed by HPLC for sugar release from the oligomers.

G. Corncob Saccharification Assay

For a typical example herein, unless otherwise specifically describedwith the particular examples, corncob saccharification was performed ina microtiter plate format in accordance with the following procedures.The biomass substrate, e.g., a dilute ammonia pretreated corncob, wasdiluted in water and pH-adjusted with sulfuric acid to create a pH 5, 7%cellulose slurry that was then used directly without further processingin the assays. Enzyme samples were loaded based on mg total protein perg of cellulose (as determined using conventional compositional analysismethods, such as, for example, using the method described in Example 1Aabove) in the substrate (e.g., the corncob). The enzymes were thendiluted in 50 mM sodium acetate, pH 5.0, to obtain the desired loadingconcentration. Forty (40) μL of enzyme solution were added to 70 mg ofdilute-ammonia pretreated corncob at 7% cellulose per well (equivalentto 4.5% cellulose final per well). The assay plates were covered withaluminum plate sealers, mixed at room temperature and incubated at 50°C., 200 rpm, for 3 days (“3d”). At the end of the incubation period, thesaccharification reaction was quenched by adding to each well 100 μL ofa 100 mM glycine buffer, pH10.0. The plate was centrifuged for 5 min at3,000 rpm. Ten (10) μL of the supernatant was then added to 200 μL ofMilliQ water in a 96-well HPLC plate and the soluble sugars weremeasured using HPLC.

Example 2 Construction of an Integrated Expression Strain of Trichodermareesei

An integrated expression strain of Trichoderma reesei was constructedthat co-expressed five genes: T. reesei β-glucosidase gene bgl1, T.reesei endoxylanase gene xyn3, F. verticillioides β-xylosidase genefv3A, F. verticillioides β-xylosidase gene fv43D, and F. verticillioidesα-arabinofuranosidase gene fv51A.

The construction of the expression cassettes for these different genesand the transformation of T. reesei are described below.

A. Construction of the β-Glucosidase Expression Vector

The N-terminal portion of the native T. reesei β-glucosidase gene bgl1was codon optimized by DNA 2.0 (Menlo Park, USA). This synthesizedportion comprised of the first 447 bases of the coding region. Thisfragment was PCR amplified using primers SK943 and SK941. The remainingregion of the native bgl1 gene was PCR amplified from a genomic DNAsample extracted from T. reesei strain RL-P37 (Sheir-Neiss, G et al.Appl. Microbiol. Biotechnol. 1984, 20:46-53), using primer SK940 andSK942. These two PCR fragments of the bgl1 gene were fused together in afusion PCR reaction, using primers SK943 and SK942:

Forward Primer SK943: (SEQ ID NO: 121)(5′-CACCATGAGATATAGAACAGCTGCCGCT-3′) Reverse Primer SK941:(SEQ ID NO: 122) (5′-CGACCGCCCTGCGGAGTCTTGCCCAGTGGTCCCGCGACAG-3′) Forward Primer (SK940): (SEQ ID NO: 123)(5′-CTGTCGCGGGACCACTGGGCAAGACTCCGCAGGGCGGTCG-3′) Reverse Primer (SK942): (SEQ ID NO: 124) (5′-CCTACGCTACCGACAGAGTG-3′) 

The resulting fusion PCR fragments were cloned into the Gateway® Entryvector pENTR™/D-TOPO®, and transformed into E. coli One Shot® TOP10Chemically Competent cells (Invitrogen) resulting in the intermediatevector, pENTR-TOPO-Bgl1-(943/942) (FIG. 8A). The nucleotide sequence ofthe inserted DNA was determined. The pENTR-943/942 vector with thecorrect bgl1 sequence was recombined with pTrex3g using a LR Clonase®reaction protocol outlined by Invitrogen. The LR clonase reactionmixture was transformed into E. coli One Shot® TOP10 ChemicallyCompetent cells (Invitrogen), resulting in the final expression vector,pTrex3g 943/942 (FIG. 8B). The vector also contains the Aspergillusnidulans amdS gene, encoding acetamidase, as a selectable marker fortransformation of T. reesei. The expression cassette was amplified byPCR with primers SK745 and SK771 to generate product for transformationof T. reesei.

Forward Primer SK771: (SEQ ID NO: 125) (5′-GTCTAGACTGGAAACGCAAC-3′)Reverse Primer SK745: (SEQ ID NO: 126) (5′-GAGTTGTGAAGTCGGTAATCC-3′)

B. Construction of the Endoxylanase Expression Cassette

The native T. reesei endoxylanase gene xyn3 was PCR amplified from agenomic DNA sample extracted from T. reesei, using primers xyn3F-2 andxyn3R-2.

Forward Primer xyn3F-2: (SEQ ID NO: 127)(5′-CACCATGAAAGCAAACGTCATCTTGTGCCTCCTGG-3′) Reverse Primer (xyn3R-2):(SEQ ID NO: 128) (5′-CTATTGTAAGATGCCAACAATGCTGTTATATGCCGGCTTG GGG-3′)

The resulting PCR fragments were cloned into the Gateway® Entry vectorpENTR™/D-TOPO®, and transformed into E. coli One Shot® TOP10 ChemicallyFIG. 8C). The nucleotide sequence of the inserted DNA was determined.The pENTR/Xyn3 vector with the correct xyn3 sequence was recombined withpTrex3g using a LR Clonase® reaction protocol outlined by Invitrogen.The LR clonase reaction mixture was transformed into E. coli One Shot®TOP10 Chemically Competent cells (Invitrogen), resulting in the finalexpression vector, pTrex3g/Xyn3 (FIG. 8D). The vector also contains theAspergillus nidulans amdS gene, encoding acetamidase, as a selectablemarker for transformation of T. reesei. The expression cassette wasamplified by PCR with primers SK745 and SK822 to generate product fortransformation of T. reesei.

Forward Primer SK745: (SEQ ID NO: 129) (5′-GAGTTGTGAAGTCGGTAATCC-3′)Reverse Primer SK822: (SEQ ID NO: 130) (5′-CACGAAGAGCGGCGATTC-3′)

C. Construction of the β-Xylosidase Fv3A Expression Vector

The F. verticillioides β-xylosidase fv3A gene was amplified from a F.verticillioides genomic DNA sample using the primers MH124 and MH125.

Forward Primer MH124: (SEQ ID NO: 131)(5′-CAC CCA TGC TGC TCA ATC TTC AG-3′) Reverse Primer MH125:(SEQ ID NO: 132) (5′-TTA CGC AGA CTT GGG GTC TTG AG-3′)

The PCR fragments were cloned into the Gateway® Entry vectorpENTR™/D-TOPO®, and transformed into E. coli One Shot® TOP10 ChemicallyCompetent cells (Invitrogen) resulting in the intermediate vector,pENTR-Fv3A (FIG. 8E). The nucleotide sequence of the inserted DNA wasdetermined. The pENTR-Fv3A vector with the correct fv3A sequence wasrecombined with pTrex6g (FIG. 8F) using a LR Clonase® reaction protocoloutlined by Invitrogen. The LR clonase reaction mixture was transformedinto E. coli One Shot® TOP10 Chemically Competent cells (Invitrogen),resulting in the final expression vector, pTrex6g/Fv3A (FIG. 8G). Thevector also contains a chlorimuron ethyl resistant mutant of the nativeT. reesei acetolactate synthase (als) gene, designated alsR, which isused together with its native promoter and terminator as a selectablemarker for transformation of T. reesei (WO2008/039370 A1). Theexpression cassette was PCR amplified with primers SK1334, SK1335 andSK1299 to generate product for transformation of T. reesei.

Forward Primer SK1334: (SEQ ID NO: 133) (5′-GCTTGAGTGTATCGTGTAAG-3′)Forward Primer SK1335: (SEQ ID NO: 134) (5′-GCAACGGCAAAGCCCCACTTC-3′)Reverse Primer SK1299: (SEQ ID NO: 135)(5′-GTAGCGGCCGCCTCATCTCATCTCATCCATCC-3′)

D. Construction of the β-Xylosidase Fv43D Expression Cassette

For the construction of the F. verticillioides β-xylosidase Fv43Dexpression cassette, the fv43D gene product was amplified from a F.verticillioides genomic DNA sample using the primers SK1322 and SK1297.A region of the promoter of the endoglucanase gene egl1 was amplified byPCR from a T. reesei genomic DNA sample extracted from strain RL-P37,using the primers SK1236 and SK1321. These two PCR amplified DNAfragments were subsequently fused together in a fusion PCR reactionusing the primers SK1236 and SK1297. The resulting fusion PCR fragmentwas cloned into pCR-Blunt II-TOPO vector (Invitrogen) to give theplasmid TOPO Blunt/Pegl1-Fv43D (FIG. 8H) and E. coli One Shot® TOP10Chemically Competent cells (Invitrogen) were transformed using thisplasmid. Plasmid DNA was extracted from several E. coli clones andconfirmed by restriction digest.

Forward Primer SK1322: (SEQ ID NO: 136) (5′-CACCATGCAGCTCAAGTTTCTGTC-3′)Reverse Primer SK1297: (SEQ ID NO: 137)(5′-GGTTACTAGTCAACTGCCCGTTCTGTAGCGAG-3′) Forward Primer SK1236:(SEQ ID NO: 138) (5′-CATGCGATCGCGACGTTTTGGTCAGGTCG-3′)Reverse Primer SK1321: (SEQ ID NO: 139)(5′-GACAGAAACTTGAGCTGCATGGTGTGGGACAACAAGAAGG-3′)

The expression cassette was PCR amplified from TOPO Blunt/Pegl1-Fv43Dwith primers SK1236 and SK1297 to generate product for transformation ofT. reesei.

E. Construction of the α-Arabinofuranosidase Expression Cassette

For the construction of the F. verticillioides α-arabinofuranosidasegene fv51A expression cassette, the fv51A gene product was amplifiedfrom F. verticillioides genomic DNA using the primers SK1159 and SK1289.A region of the promoter of the endoglucanase gene egl1 was amplified byPCR from a T. reesei genomic DNA sample extracted from strain RL-P37,using the primers SK1236 and SK1262. These two PCR amplified DNAfragments were subsequently fused together in a fusion PCR reactionusing the primers SK1236 and SK1289. The resulting fusion PCR fragmentwas cloned into pCR-Blunt II-TOPO vector (Invitrogen) to give theplasmid TOPO Blunt/Pegl1-Fv51A (FIG. 8I) and E. coli One Shot® TOP10Chemically Competent cells (Invitrogen) were transformed using thisplasmid.

Forward Primer SK1159: (SEQ ID NO: 140)(5′-CACCATGGTTCGCTTCAGTTCAATCCTAG-3′) Reverse Primer SK1289:(SEQ ID NO: 141) (5′-GTGGCTAGAAGATATCCAACAC-3′) Forward Primer SK1236:(SEQ ID NO: 142) (5′-CATGCGATCGCGACGTTTTGGTCAGGTCG-3′)Reverse Primer SK1262: (SEQ ID NO: 143)(5′-GAACTGAAGCGAACCATGGTGTGGGACAACAAGAAGGAC-3′)

The expression cassette was PCR amplified with primers SK1298 and SK1289to generate product for transformation of T. reesei.

Forward Primer SK1298: (SEQ ID NO: 144) (5′-GTAGTTATGCGCATGCTAGAC-3′)Reverse Primer SK1289: (SEQ ID NO: 145) (5′-GTGGCTAGAAGATATCCAACAC-3′)

F. Co-Transformation of T. Reesei Expression Cassettes for β-Glucosidaseand Endoxylanase

A Trichoderma reesei mutant strain, derived from RL-P37 (Sheir-Neiss, Get al. Appl. Microbiol. Biotechnol. 1984, 20:46-53), and selected forhigh cellulase production was co-transformed with the β-glucosidaseexpression cassette (cbh1 promoter, T. reesei β-glucosidase1 gene, cbh1terminator, and amdS marker), and the endoxylanase expression cassette(cbh1 promoter, T. reesei xyn3, and cbh1 terminator) using PEG-mediatedtransformation (Penttila, M et al. Gene 1987, 61(2):155-64). Numeroustransformants were isolated and examined for β-glucosidase andendoxylanase production. One transformant called T. reesei strain #229was used for transformation with the other expression cassettes.

G. Co-Transformation of T. Reesei Strain #229 with Expression Cassettesfor Two β-Xylosidases and an α-Arabinofuranosidase

T. reesei strain #229 was co-transformed with the β-xylosidase fv3Aexpression cassette (cbh1 promoter, fv3A gene, cbh1 terminator, and alsRmarker), the β-xylosidase fv43D expression cassette (egl1 promoter,fv43D gene, native fv43D terminator), and the fv51Aα-arabinofuranosidase expression cassette (egl1 promoter, fv51A gene,fv51A native terminator) using electroporation (see e.g. WO 08153712).Transformants were selected on Vogels agar plates containing chlorimuronethyl (80 ppm). Vogels agar was prepared as follows, per liter.

50 x Vogels Stock Solution (recipe below) 20 mL BBL Agar 20 g Withdeionized H₂O bring to 980 mL post-sterile addition: 50% Glucose 20 mL50 x Vogels Stock Solution, per liter: In 750 mL deionized H2O, dissolvesuccessively: Na₃Citrate*2H₂O 125 g KH₂PO₄ (Anhydrous) 250 g NH₄NO₃(Anhydrous) 100 g MgSO₄*7H₂O 10 g CaCl₂*2H₂O 5 g Vogels Trace ElementSolution (recipe below) 5 mL d-Biotin 0.1 g With deionized H₂O, bring to1 L Vogels Trace Element Solution: Citric Acid 50 g ZnSO₄•*7H₂O 50 gFe(NH₄)2SO₄•*6H₂O 10 g CuSO₄•5H₂O 2.5 g MnSO₄•4H₂O 0.5 g H₃BO₃ 0.5 gNa₂MoO₄•2H₂O 0.5 g

Numerous transformants were isolated and examined for β-xylosidase andL-α-arabinofuranosidase production. Transformants were also screened forbiomass conversion performance according to the cob saccharificationassay described in Example 1 (supra). Examples of T. reesei integratedexpression strains described herein are H3A, 39A, A10A, 11A, and G9A,which express all of the genes for T. reesei beta-glucosidase 1, T.reesei Xyn3, Fv3A, Fv51A, and Fv43D, at different ratios. Otherintegrated T. reesei strains include those wherein most of the genes forT. reesei beta-glucosidase 1, T. reesei Xyn3, Fv3A, Fv51A, and Fv43D,were expressed at different ratios. For example, one lackedoverexpressed T. reesei Xyn3; another lacked Fv51A, as determined byWestern Blot; two others lacked Fv3A, one lacked overexpressed Bgl1(e.g. strain H3A-5).

H. Composition of T. reesei Integrated Strain H3A

Fermentation of the T. reesei integrated strain H3A yields the followingproteins T. reesei Xyn3, T. reesei Bgl 1, Fv3A, Fv51A, and Fv43D, atratios determined as described herein and shown in FIG. 9.

I. Protein Analysis by HPLC

Liquid chromatography (LC) and mass spectroscopy (MS) were performed toseparate, identify, and quantify the enzymes contained in fermentationbroths. Enzyme samples were first treated with a recombinantly expressedendoH glycosidase from S. plicatus (e.g., NEB P0702L). EndoH was used ata ratio of 0.01-0.03 μg endoH protein per Kg sample total protein andincubated for 3 h at 37° C., pH 4.5-6.0 to enzymatically remove N-linkedgycosylation prior to HPLC analysis. Approximately 50 μg of protein wasthen injected for hydrophobic interaction chromatography using anAgilent 1100 HPLC system with an HIC-phenyl column and a high-to-lowsalt gradient over 35 min. The gradient was achieved using high saltbuffer A: 4 M ammonium sulphate containing 20 mM potassium phosphate pH6.75 and low salt buffer B: 20 mM potassium phosphate pH 6.75. Peakswere detected with UV light at 222 nm and fractions were collected andidentified by mass spectroscopy. Protein concentrations are reported asthe percent of each peak area relative to the total integrated area ofthe sample.

J. Effect of Addition of Purified Proteins to the Fermentation Broth ofT. Reesei Integrated Strain H3A on Saccharification of Dilute AmmoniaPretreated Corncob

Purified proteins (and one unpurified protein) were serially dilutedfrom stock solution and added to a fermentation broth of T. reeseiintegrated strain H3A to determine their benefit to saccharification ofpretreated biomass. Dilute ammonia pretreated corncob was loaded intomicrotiter plate (MTP) wells at 20% solids (w/w) (˜5 mg of cellulose perwell), pH 5. H3A protein (in the form of fermentation broth) was addedto each well at 20 mg protein/g cellulose. Volumes of 10, 5, 2, and 1 μLof each of the diluted proteins (FIG. 10) were added into individualwells, and water was added such that the liquid addition to each wellwas a total of 10 μL. Reference wells included additions of either 10 μLwater or dilutions of additional H3A fermentation broth. The MTP weresealed with foil and incubated at 50° C. with 200 RPM shaking in anInnova incubator shaker for three days. The samples were quenched with100 μL of 100 mM glycine pH 10. The quenched samples were covered with aplastic seal and centrifuged 3000 RPM for 5 min at 4° C. An aliquot (5μL) of the quenched reactions was diluted with 100 μL of water and theconcentration of glucose produced in the reactions was determined usingHPLC. The glucose data was plotted as a function of the proteinconcentration added to the 20 mg/g of H3A (the concentrations of theprotein additions were variable due to different starting concentrationsand additions by volume). Results are shown in FIGS. 11A-11D.

Example 3 Construction of T. reesei Strains

A. Construction of and Screening for T. Reesei Strain H3A/EG4#27

An expression cassette containing the T. reesei egl1 (also termed “Cel7B”) promoter, T. reesei eg4 (also termed “TrEG4”, or “Cel 61A”) openreading frame, and cbh1 (Cel 7A) terminator sequence (FIG. 12A) fromTrichoderma reesei, and sucA selectable marker (see, Boddy et al., Curr.Genet. 1993, 24:60-66) from Aspergillus niger was cloned into pCR BluntII TOPO (Invitrogen) (FIG. 12B).

The expression cassette Pegl1-eg4-sucA was amplified by PCR with theprimers:

(SEQ ID NO: 146) SK1298: 5′-GTAGTTATGCGCATGCTAGAC-3′ (SEQ ID NO: 147)214: 5′-CCGGCTCAGTATCAACCACTAAGCACAT-3′

Pfu Ultra II (Stratagene) was used as the polymerase for the PCRreaction. The products of the PCR reaction were purified with theQIAquick PCR purification kit (Qiagen) as per the manufacturer'sprotocol. The products of the PCR reaction were then concentrated usinga speed vac to 1-3 μg/μL. The T. reesei host strain to be transformed(H3A) was grown to full sporulation on potato dextrose agar plates for 5d at 28° C. Spores from 2 plates were harvested with MilliQ water andfiltered through a 40 μM cell strainer (BD Falcon). Spores weretransferred to a 50 mL conical tube and washed 3 times by repeatedcentrifugation with 50 mL water. A final wash with 1.1 M sorbitolsolution was carried out. The spores were resuspended in a small volume(less than 2 times the pellet volume) using 1.1 M sorbitol solution. Thespore suspension was then kept on ice. Spore suspension (60 μL) wasmixed with 10-20 μg of DNA, and transferred into the electroporationcuvette (E-shot, 0.1 cm standard electroporation cuvette fromInvitrogen). The spores were electroporated using the Biorad Gene PulserXcell with settings of 16 kV/cm, 25 μF, 400Ω. After electroporation, 1mL of 1.1.M sorbitol solution was added to the spore suspension. Thespore suspension was plated on Vogel's agar (see example 2G), containing2% sucrose as the carbon source.

The transformation plates were incubated at 30° C. for 5-7 d. Theinitial transformants were restreaked onto secondary Vogel's agar plateswith sucrose and grown at 30° C. for an additional 5-7 d. Singlecolonies growing on secondary selection plates were then grown in wellsof microtiter plates using the method described in WO/2009/114380. Thesupernatants were analyzed on SDS-PAGE to check for expression levelsprior to saccharification performance screening.

A total of 94 transformants overexpressed EG4 in strain H3A. Two H3Acontrol strains were grown in microtiter plates along with the H3A/EG4strains. Performance screening of T. reesei strains expressing EG4protein was performed using ammonia pretreated corncob. The diluteammonia pretreated corncob was suspended in water and adjusted to pH 5.0with sulfuric acid to achieve 7% cellulose. The slurry was dispensedinto a flat bottom 96 well microtiter plate (Nunc, 269787) andcentrifuged at 3,000 rpm for 5 min.

Corncob saccharification reactions were initiated by adding 20 μL of H3Aor H3A/EG4 strain culture broth per well of substrate. The corncobsaccharification reactions were sealed with aluminum (E&K scientific)and mixed for 5 min at 650 rpm, 24° C. The plate was then placed in anInnova incubator at 50° C. and 200 rpm for 72 h. At the end of 72-hsaccharification, the reactions were quenched by adding 100 μL of 100 mMglycine, pH 10.0. The plate was then mixed thoroughly and centrifuged at3,000 rpm for 5 min. Supernatant (10 μL) was added to 200 μL of water inan HPLC 96-well microtiter plate (Agilent, 5042-1385). Glucose, xylose,cellobiose and xylobiose concentrations were measured by HPLC using anAminex HPX-87P column (300 mm×7.8 mm, 125-0098) pre-fitted with guardcolumn.

The screening on corncob identified the following H3A/EG4 strains ashaving improved glucan and xylan conversion compared to the H3A controlstrains: 1, 2, 3, 4, 5, 6, 14, 22, 27, 43, and 49 (FIG. 13).

Select H3A/EG4 strains were re-grown in shake flasks. A total of 30 mLof protein culture filtrate was collected per shake flask per strain.The culture filtrates were concentrated 10-fold using 10 kDa membranecentrifugal concentrators (Sartorious, VS2001) and the total proteinconcentration was determined by BCA as described in Example 1C. Acorncob saccharification reaction was performed using 2.5, 5, 10, or 20mg protein from H3A/EG4 strain samples per g of cellulose per well ofcorncob substrate. An H3A strain produced at 14 L fermentation scale anda previously identified low performance sample (H3A/EG4 strain #20)produced at shake flask scale were included as controls. Thesaccharification reactions were carried out as described in Example 4(below). Increased glucan conversion with increased protein dose wasobserved with culture supernatant from all of the EG4 expressing strains(FIG. 14). T. reesei integrated strain H3A/EG4#27 was used in additionalsaccharification reactions, and the strain was purified by streaking asingle colony onto a potato dextrose plate from which a single colonywas isolated.

Example 4 Range of T. Reesei EG4 Concentrations for ImprovedSaccharification of Dilute Ammonia Pretreated Corncob

To determine preferred dosing, hydrolysis of dilute ammonia pretreatedcorncob (25% solids, 8.7% cellulose, 7.3% xylan) was conducted at pH 5.3using fermentation broth from either T. reesei integrated strain H3A/EG4#27 or H3A with purified EG4 added to the reaction mix. The totalloading of T. reesei integrated strain H3A/EG4 #27 or H3A was 14 mgprotein per gram of glucan (G) and xylan (X).

The reaction mix (total mass 5 g) was loaded into 20 mL scintillationvials in a total reaction volume of 5 mL according to the dosing chartin FIGS. 15, 17A and 17B.

The set up for experiment 1 is shown in FIG. 15. MilliQ Water and 6 NSulfuric acid were mixed in a conical tube and added to the respectivevials and the vials were swirled to mix the contents. Enzymes sampleswere added to the vials and the vials incubated for 6 d at 50° C. Atvarious time points, 100 μL of sample was removed from the vialssdiluted with 900 μL 5 mM sulfuric acid, vortexed, centrifuged and thesupernatant was used to measure the concentrations of soluble sugarsusing HPLC. The results of glucan and xylan conversion are shown inFIGS. 16A and 16B, respectively.

The set up for experiment 2 is shown in FIG. 17A. To further determinethe preferred EG4 concentration, saccharification of dilute ammoniacorncob (25% solids, 8.7% cellulose, 7.3% xylan) was conducted at pH 5.3using fermentation broth from either T. reesei integrated strain H3A/EG4#27 or H3A with purified EG4 added (ranging from 0.05 to 1.0 mgprotein/g G+X) to the reaction mix. The total loading of T. reeseiintegrated strain H3A/EG4 #27 or H3A was 14 mg protein/g glucan+xylan.The experimental results are shown in FIG. 18A.

The set up for experiment 3 is shown in FIG. 17B. To pinpoint thepreferred concentration range of T. reesei Eg4 yet further, diluteammonia corncob (25% solids, 8.7% cellulose, and 7.3% xylan) washydrolyzed at pH 5.3 using T. reesei integrated strain H3A/EG4 #27 orH3A with purified EG4 added at concentrations ranging from 0.1-0.5 mgprotein/g G+X. The total loading of T. reesei integrated strain H3A/EG4#27 or H3A was 14 mg protein per g of glucan and xylan.

Results are shown in FIG. 18B.

Example 5 Effect of T. Reesei Eg4 on Saccharification of Dilute AmmoniaPretreated Corn Stover at Different Solid Loadings

Dilute ammonia pre-treated corn stover was incubated with fermentationbroth from T. reesei integrated strain H3A or H3A/EG4#27 (14 mgprotein/g glucan and xylan) at 7, 10, 15, 20 and 25% solids (% S) forthree days at 50° C., pH 5.3 (5 g total wet biomass in 20 mL vials). Thereactions were carried out as described in Example 4 above. Glucose andxylose were analyzed by HPLC. Results are shown in FIG. 19. All samplesup to 20% solids were visibly liquefied on day 1.

Example 6 Effect of Overexpression of T. Reesei EG4 on Hydrolysis ofDilute Ammonia Pretreated Corncob

The effect of overexpression of T. reesei Eg4 in strain H3A onsaccharification of dilute ammonia pretreated corncob was tested usingfermentation broths from strains H3A/EG4 #27 and H3A. Corncobsaccharification at 3 g scale was performed in 20 mL glass vials asfollows. Enzyme preparation, 1 N sulfuric acid and 50 mM pH 5.0 sodiumacetate buffer (with 0.01% sodium azide and 5 mM MnCl₂) were added togive a final slurry of 3 g total reaction, 22% dry solids, pH 5.0 withenzyme loadings varying between 1.7 and 21.0 mg total protein per gramGlucan+Xylan. All saccharification vials were incubated at 48° C. with180 rpm rotation. After 72 h, 12 mL of filtered MilliQ water was addedto each vial to dilute the entire saccharification reaction 5-fold. Thesamples were centrifuged at 14,000×g for 5 min, then filtered through a0.22 μm nylon filter (Spin-X centrifuge tube filter, CorningIncorporated, Corning, N.Y.) and further diluted 4-fold with filteredMilliQ water to create a final 20× dilution. 20 μL injections wereanalyzed by HPLC to measure the sugars released.

Overexpression or addition of T. reesei Eg4 led to enhanced xylose andglucose monomer release as compared to H3A alone (FIGS. 20 and 21).Addition of H3A/EG4#27 at different doses led to an increased yield ofxylose as compared to strain H3A, or compared to Eg4+a constant 1.12 mgXyn3 per g Glucan+Xylan (FIG. 20).

Addition of H3A/EG4#27 at different doses led to an increased yield ofglucose compared to strain H3A or compared to Eg4+a constant 1.12 mgXyn3 per g Glucan+Xylan (FIG. 21).

The effect of T. reesei Eg4 on total fermentable monomer (xylose,glucose and arabinose) release by integrated strains H3A/EG4#27 or H3Ais illustrated in the FIG. 22. The H3A/EG4#27 integrated strain led toenhanced total fermentable monomer release compared to the integratedstrain H3A, or compared to Eg4+1.12 mg Xyn3/g Glucan+Xylan.

Example 7 Purified T. Reesei EG4 Leads to Glucose Release in DiluteAmmonia Pretreated Corncob

The effect of purified T. reesei Eg4 on the concentration of sugarsreleased was tested using 1.05 g dilute ammonia pretreated corncob inthe presence or absence of 0.53 mg Xyn3 per g Glucan+Xylan. Theexperiments were performed as described in Example 6. Results are shownin FIG. 23. The data indicate that purified T. reesei Eg4 leads torelease of glucose monomer without the action of other cellulases suchas endoglucanases, cellobiohydrolases and β-glucosidases.

Saccharification experiments were also conducted using dilute ammoniapretreated corncob with purified Eg4 added alone (no Xyn3 added). 3.3 μLof purified Eg4 (15.3 mg/mL) was added to 872 μL 50 mM, pH 5.0 sodiumacetate buffer (included 0.01% sodium azide and 5 mM MnCl₂), 165 mg ofdilute ammonia pretreated corncob (67.3% dry solids, 111 mg dry solidsadded) and 16.5 μL of 1 N sulfuric acid in 5 mL vials. The vials wereincubated at 48° C. and rotated at 180 rpm. Periodically, 20 μL aliquotswere removed, diluted 10-fold with filter sterilized double distilledwater and filtered through a nylon filter before analysis for glucosereleased on a Dionex Ion Chromatography system. Authentic glucosesolutions were used as external standards. Results are shown in FIG. 24,indicating that addition of purified Eg4 leads to release of glucosemonomer from dilute ammonia pretreated corncobs over 72 h incubation at48° C. in the absence of other cellulases or endoxylanase.

Example 8 Saccharification Performance of T. Reesei Integrated StrainsH3A and H3A/EG4 #27 on Various Substrates

In this experiment, fermentation broth from T. reesei integrated strainH3A or H3A/EG4#27, dosed at 14 mg protein per g of glucan+xylan, wastested for saccharification performance on different substratesincluding: dilute ammonia pretreated corncob, washed dilute ammoniapretreated corncob, ammonia fiber expanded corn stover (AFEX CS), SteamExpanded Sugarcane Bagasse (SEB), and Kraft-pretreated paper pulps FPP27(Softwood Industrial Unbleached Pulp delignified-Kappa 13.5, Glucan81.9%, Xylan 8.0%, Klason Lignin 1.9%), FPP-31 (Hardwood Unbleached Pulpdelignified-Kappa 10.1, Glucan 75.1%, Xylan 19.1%, Klason Lignin 2.2%),and FPP-37 (Softwood Unbleached Pulp air dried-Kappa 82, Glucan 71.4%,Xylan 8.7%, Klason Lignin 11.3%).

The saccharification reactions were set up in 25 mL glass vials withfinal mass of 10 g in 0.1 M Sodium Citrate Buffer, pH 5.0 and incubatedat 50° C., 200 rpm for 6 d. At the end of 6 d, 100 μL aliquots werediluted 1:10 in 5 mM sulfuric acid and the samples analyzed by HPLC todetermine glucose and xylose formation. Results are shown in FIG. 25.

Example 9 Effect of T. Reesei EG4 on Saccharification of Acid PretreatedCorn Stover

The effect of Eg4 on saccharification of acid pretreated corn stover wastested. Corn stover pretreated with dilute sulfuric acid (Schell, D J,et al., Appl. Biochem. Biotechnol. 2003, 105(1-3):69-85) was obtainedfrom NREL, adjusted to 20% solids and conditioned to a pH 5.0 with theaddition of soda ash solution. Saccharification of the pretreatedsubstrate was performed in a microtiter plate using 20% total solids.Total protein in the fermentation broths was measured by the Biuretassay (see Example 1 above). Increasing amounts of fermentation brothfrom T. reesei integrated strains H3A/EG4 #27 and H3A were added to thesubstrate and saccharification performance was measured followingincubation at 50° C., 5 d, 200 RPM shaking. Glucose formation (mg/g) wasmeasured using HPLC. Results are shown in FIG. 26.

Example 10 Saccharification Performance of T. Reesei Integrated StrainsH3A and H3A/EG4#27 on Dilute Ammonia Pretreated Corn Leaves, Stalks, andCobs

Saccharification performance of T. reesei integrated strains H3A andH3A/EG4#27 was compared on dilute ammonia pretreated corn stover leaves,stalks, or cobs. Pretreatment was performed as described in WO06110901A.Five (5) g total mass (7% solids) was hydrolyzed in 20 mL vials at pH5.3 (pH adjusted with 6 NH₂SO₄) using 14 mg protein per g ofglucan+xylan. Saccharification reactions were carried out at 50° C. andsamples analyzed by HPLC for glucose and xylose released on day 4.Results are shown in FIG. 27.

Example 11 Saccharification Performance on Dilute Ammonia PretreatedCorncob in Response to Overexpressed EG4 from T. Reesei

Saccharification reactions at 3 g scale were performed using diluteammonia pretreated corncob. Sufficient pretreated cob preparation wasmeasured into 20 mL glass vials to give 0.75 g dry solid. Enzymepreparation, 1 N sulfuric acid and 50 mM pH 5.0 sodium acetate buffer(with 0.01% sodium azide) were added to give final slurry of 3 g totalreaction, 25% dry solids, pH 5.0. Extra cellular protein (fermentationbroth) from the T. reesei integrated strain H3A was added at 14 mgprotein/g (glucan+xylan) either with or without an additional 5% of the14 mg protein load as the unpurified culture supernatant from a T.reesei strain (Δcbh1 Δcbh2 Δeg1 Δeg2) (See International publication WO05/001036) over expressing Eg4. The saccharification reactions wereincubated for 72 h at 50° C. Following incubation, the reaction contentswere diluted 3-fold, filtered and analyzed by HPLC for glucose andxylose concentration. The results are shown in FIG. 28. Addition of Eg4protein in the form of extracelluar protein from a T. reesei strain overexpressing Eg4 to H3A substantially increased the release of monomerglucose and slightly increased the release of monomer xylose.

Example 12 Saccharification Performance of Strain H3A/EG4#27 on AmmoniaPretreated Switchgrass

The saccharification performance of strain H3A/EG4#27 on ammoniapretreated switchgrass (International Patent Publication WO06110901A) atincreasing protein doses was compared to that of strain H3A (18.5%solids). Pretreated switchgrass preparations were measured into 20 mLglass vials to give 0.925 g of dry solid. 1 N sulfuric acid and 50 mM pH5.3 sodium acetate buffer (with 0.01% sodium azide) were added to givefinal slurry of 5 grams total reaction. The enzyme dosages of H3A testedwere 14, 20, and 30 mg/g (glucan+xylan); and the dosages of H3A-EG4 #27were 5, 8, 11, 14, 20, and 30 mg/g (glucan+xylan). The reactions wereincubated at 50° C. for 3 d. Following incubation, the reaction contentswere diluted 3-fold, filtered and analyzed by HPLC for glucose andxylose concentration. The conversion of glucan and xylan were calculatedbased on the composition of the switchgrass substrate. The results (FIG.29) indicate that the performance of H3A-EG4 #27 is more effective forglucan conversion than H3A at the same enzyme dosages.

Example 13 Effect of T. Reesei EG4 Additions on Corncob Saccharificationand on CMC and Cellobiose Hydrolysis

A. Corncob Saccharification:

Dilute ammonia pretreated corncob was adjusted to 20% solids, 7%cellulose and 65 mg was dispensed per well in a microtiter plate.Saccharification reactions were initiated by adding 35 μL of 50 mMsodium acetate (pH 5.0) buffer containing T. reesei CBH1 at 5 mgprotein/g glucan (final) and the relevant enzymes (CBH1 or Eg4), atfinal concentrations of 0, 1, 2, 3, 4 and 5 mg/g glucan. An Eg4 controlreceived only EG4 at the same doses and as such, the total added proteinin these wells was less. The microtiter plates were sealed with analuminum plate seal (E&K scientific) and mixed for 2 min at 600 rpm, 24°C. The plate was then placed in an Innova incubator at 50° C. and 200rpm for 72 h.

At the end of 72-h saccharification, the plate was quenched by adding100 μL of 100 mM glycine, pH 10.0. The plate was then centrifuged at3000 rpm for 5 min Supernatant (20 μL) was added to 100 μL of water inHPLC 96 well microtiter plate (Agilent 5042-1385). Glucose andcellobiose concentrations were measured by HPLC using Aminex HPX-87Pcolumn (300 mm×7.8 mm, 125-0098) pre-fitted with guard column. % glucanconversion was calculated by 100×(mg cellobiose+mg glucose)/total glucanin substrate (FIG. 30).

B. CMC Hydrolysis:

Carboxymethylcellulose (CMC, Sigma C4888) was diluted to 1% with 50 mMSodium Acetate, pH 5.0. Hydrolysis reactions were initiated byseparately adding each of three T. reesei purified enzymes—EG4, EG1 andCBH1 at final concentrations of 20, 10, 5, 2.5, 1.25 and 0 mg/g to 100μL of 1% CMC in a 96-well microtiter plate (NUNC #269787). Sodiumacetate, pH 5.0 50 mM was added to each well to a final volume of 150μL. The CMC hydrolysis reactions were sealed with an aluminum plate seal(E&K scientific) and mixed for 2 min at 600 rpm, 24° C. The plate wasthen placed in an Innova incubator at 50° C. and 200 rpm for 30 min.

At the end of 30 min. incubation, the plate was put in ice water for 10min. to stop the reaction, and samples were transferred to eppendorftubes. To each tube was added 375 μL of dinitrosalicylic acid (DNS)solution (see below). Samples were then boiled for 10 min and O.D wasmeasured at 540 nm by SpectraMAX 250 (Molecular Devices). Results areshown in FIG. 31.

DNS Solution:

40 g 3.5-Dinitrosalicylic acid (Sigma, D0550)

8 g Phenol

2 g Sodium sulfite (Na₂SO₃)800 g Na—K tartarate (Rochelle salt)Add all the above to 2 L of 2% NaOHStir overnight, covered with aluminum foilAdd distilled deionized water to a final volume of 4 LMix wellStore in a dark bottle, refrigerated

C. Cellobiose Hydrolysis

Cellobiose was diluted to 5 g/L with 50 mM Sodium Acetate, pH 5.0.Hydrolysis reactions were initiated by separately adding each of twoenzymes—EG4 and BGL1 at final concentrations of 20, 10, 5, 2.5, and 0mg/g to 100 μL cellobiose solution at 5 g/L. Sodium acetate, pH 5.0 wasadded to each well to a final volume of 120 μL. The reaction plates weresealed with an aluminum plate seal (E&K scientific) and mixed for 2 minat 600 rpm, 24° C. The plate was then placed in an Innova incubator at50° C. and 200 rpm for 2 h.

At the end of the 2 h hydrolysis step, the plate was quenched by adding100 μL of 100 mM glycine, pH 10.0. The plate was then centrifuged at3000 rpm for 5 min Glucose concentration was measured by ABTS(2,2′-azino-bis 3-ethylbenzothiazoline-6-sulfonic acid) assay (Example1). Ten (10) μL of supernatant was added to 90 μL ABTS solution in a96-well microtiter plate (Corning costar 9017 EIA/RIA plate, 96 wellflat bottom, medium binding). OD 420 nm was measured by SpectraMAX 250,Molecular Devices. Results are shown in FIG. 32.

Example 14 Purified EG4 Improves Glucose Production from Dilute AmmoniaPretreated Corncob when Mixed with Various Cellulase Mixtures

The effect of purified Eg4 combined with purified cellulases (T. reeseiEG1, EG2, CBH1, CBH2, and Bgl1) on the concentration of sugars releasedwas tested using 1.05 g dilute ammonia pretreated corncob in thepresence of 0.53 mg T. reesei Xyn3 per g of Glucan+Xylan. 1.06-greactions were set up in 5 mL vials containing 0.111 g dry cob solids(10.5% solids). Enzyme preparation (FIG. 33), 1N sulfuric acid and 50 mMpH 5.0 sodium acetate buffer (with 0.01% sodium azide and 5 mM MnCl₂)were added to give the final reaction weight. The reaction vials wereincubated at 48° C. with 180 rpm rotation. After 72 h, filtered MilliQwater was added to dilute each saccharification reaction by 5-fold. Thesamples were centrifuged at 14,000×g for 5 min, then filtered through a0.22 μm nylon filter (Spin-X centrifuge tube filter, CorningIncorporated, Corning, N.Y.) and further diluted 4-fold with filteredMilli-Q water to create a final 20× dilution. Twenty (20) μL injectionswere analyzed by HPLC to measure the sugars released (glucose,cellobiose, and xylose).

FIG. 34 shows glucose (A), glucose+cellobiose (B), or xylose (C)produced with each combination. Purified Eg4 improved the performance ofindividual cellulases and mixtures. When all of the purified cellulaseswere present, addition of 0.53 mg Eg4 per g Glucan+Xylan improved theconversion by almost 40%. Improvement was also seen when Eg4 was addedto a combination of CBH1, Egl1 and Bgl1. When individual cellulases werepresent with the cob, the absolute amounts of total glucose release weresubstantially lower than resulted from the experiment whereincombinations of cellulases were present with the cob, but in each case,the percent improvement in the presence of Eg4 was significant. Additionof T. reesei Eg4 to purified cellulases resulted in the followingpercent improvements in total Glucose release-Bgl1 (121%), Eg12 (112%),CBH2 (239%) and CBH1 (71%). This shows that Eg4 had a significant andbroad effect to improve cellulase performance on biomass.

Example 15 Effects Observed When EG4 was Mixed with CBH1, CBH2, andEG2—Substrate: Dilute Ammonia Pretreated Corncob

Dilute ammonia pretreated corncob saccharification reactions wereprepared by adding enzyme mixtures as follows to corncob (65 mg per wellof 20% solids, 7% cellulose) in 96-well MTPs (VWR). Eighty (80) μL of 50mM sodium acetate (pH 5.0), 1 mg Bgl1/g glucan, and 0.5 mg Xyn3/g glucanbackground were also added to all wells.

To test the effect of mixing Eg4 individually with CBH1, CBH2 and EG2,each of CBH1, CBH2, and EG2 was added at 0, 1.25, 2.5, 5, 10 and 20 mg/gglucan, and EG4 was added at concentrations of 20, 18.75, 17.5, 15, 10and 0 mg/g glucan to the respective wells, making the total proteins inindividual wells 20 mg/g glucan. The control wells received only CBH1 orCBH2 or EG2 or EG4 at the same doses, as such the total added proteinsin these wells were less than 20 mg/g.

To test the effect of Eg4 on combinations of cellulases, mixtures ofCBH1, CBH2 and EG2 at different ratios (see, FIG. 35) were added at 0,1.25, 2.5, 5, 10 and 20 mg protein/g glucan, and EG4 was added to themixtures at concentrations of 20, 18.75, 17.5, 15, 10 and 0 mg protein/gglucan, such that the total proteins in individual wells was 20 mgprotein/g glucan. As above, control wells received only one addedprotein so the total protein addition was less than 20 mg protein/g.

The corncob saccharification reactions were sealed with an aluminumplate seal (E&K scientific) and mixed for 2 min at 600 rpm, 24° C. Theplate was then placed in an Innova 44 incubator shaker (New BrunswickScientific) at 50° C. and 200 rpm for 72 h. At the end of the 72-hsaccharification step, the plate was quenched by adding 100 μL of 100 mMglycine, pH 10.0. The plate was then centrifuged at 3000 rpm for 5 min(Rotanta 460R Centrifuge, Hettich Zentrifugen). Twenty (20) μL ofsupernatant was added to 100 μL of water in an HPLC 96-well microtiterplate (Agilent, 5042-1385). Glucose and cellobiose concentrations weremeasured by HPLC using an Aminex HPX-87P column (300 mm×7.8 mm,125-0098) and guard column (BioRad).

The results were indicated in the table of FIG. 36, wherein the glucanconversion (%) is defined as 100×(glucose+cellulobiose)/total glucan.

This experiment indicates that Eg4, when added to a CBH1, CBH2 and/orEG2, was beneficial in improving saccharification of dilute ammoniapretreated corncob. Moreover, the highest improvement was observed whenEg4 and the other enzyme (CBH1, CBH2, or EG2) were added to thesaccharification mixture in an equal amount. It was also observed thatthe effect of Eg4 is substantial on the CBH1 and CBH2 mixture. Theoptimum improvement by Eg4 was observed when the amount of Eg4 to CBH1and CBH2 was 1:1.

Example 16 EG4 Improves Saccharification Performance of VariousCellulase Compositions

The total protein concentration of commercial cellulase enzymepreparations Spezyme® CP, Accellerase®1500, and Accellerase®DUET(Genencor Division, Danisco US) were determined by the modified Biuretassay (described herein).

Purified T. reesei EG4 was added to each enzyme preparation, and thesamples were then assayed for saccharification performance using a 25%solids loading of ammonia pretreated corncob, at a dose of 14 mg oftotal protein per g of substrate glucan and xylan (5 mg EG4 per g ofglucan and xylan, plus 9 mg whole cellulase per g of glucan and xylan).The saccharification reaction was carried out using 5 g of totalreaction mixture in a 20 mL vial at pH 5, with incubation at 50° C. in arotary shaker set to 200 rpm for 7 d. The saccharification samples werediluted 10× with 5 mM sulfuric acid, filtered through a 0.2 μm filterbefore injection into the HPLC. HPLC analysis was performed using aBioRad Aminex HPX-87H ion exclusion column (300 mm×7.8 mm).

Substitution of purified EG4 into whole cellulases improved glucanconversion in all tested cellulase products as illustrated in FIG. 40.As illustrated in FIG. 41, xylan conversion did not appear to beaffected by the Eg4 substitution.

Example 17 Reduction of Viscosity in Biomass Saccharification

Biomass used in this experiment was Inbicon acidified steam-expansionpretreated wheat straw, with the following composition (Table 2):

Inbicon wheat straw Component ID Mean Glucan 55.0% Xylan 5.0% GalactanArabinan Mannan Klason Lignin 31.0% Acid soluble lignin Ash 4.0% StarchMass Balance Closure 95.0%

The pre-treated wheat straw was diluted into water and pH-adjusted withsulfuric acid to pH5.0, and a solid level of 10.5% of that was mixedwith, in a first sample, a fermentation broth of a T. reesei H3A strain(FIG. 9) at a total protein concentration of 20.5 mg protein/g cellulosein the biomass substrate at 50° C., or in a second sample, thefermentation broth of T. reesei H3A (FIG. 9) at a total proteinconcentration of 18.5 mg protein/g cellulose in the biomass substrate,and 2 mg/g cellulose of purified T. reesei Eg4. Viscosity reduction wasmeasured using a Brookfield viscometer (Brookfield Engineering, Inc),monitoring viscosity change up to about 6 h. Results are indicated inFIG. 42.

Example 18 Reduction of Viscosity in Biomass Saccharification

Biomass used in this experiment was dilute acid pretreated corn stoverfrom NREL (unwashed PCS).

The unwashed pretreated corn stover was mixed, at a temperature of 50°C., pH of 5.0, and a solid level of 20% dry solids with, in a firstsample, a fermentation broth of a T. reesei H3A strain (FIG. 9) at atotal protein concentration of 20 mg/g cellulose in the biomasssubstrate, and in a second sample, a fermentation broth of T. reeseiH3A/Eg4 #27 integrated strain, also at 20 mg/g cellulose. Viscosityreduction was measured using a Brookfield viscometer (BrookfieldEngineering, Inc.), monitoring viscosity change for up to over 160 h.The results are indicated in FIG. 43.

Example 19 Reduction of Viscosity in Biomass Saccharification

Biomass used in this experiment was dilute ammonia pretreated corncob.

The dilute ammonia pretreated corncob was mixed with enzyme compositionsat two solid loading conditions: 25% dry solids and 30% dry solids.Specifically, the pretreated biomass was mixed at 50° C. and pH 5.0 with14 mg protein/g cellulose from a fermentation broth of either a T.reesei H3A (FIG. 9) or H3A/Eg4 #27 strain. Viscosity reduction wasmeasured using a Brookfield Viscometer (Brookfield Engineering, Inc.).The results are indicated in FIG. 44.

Example 20 Determining the Effects of Various Cellulases on ViscosityReduction and Glucose Production in Saccharification Process

This study used various viscosity reducing enzymes, such as OPTIMASH™BG, OPTIMASH™ TBG, OPTIMASH™ VR; or beta-glucosidase such asAccellerase® BG, in the presence of Accellerase® DUET in thesaccharification process and determined the effects of these viscosityreducing enzymes in glucose production and viscosity reduction. Enzymecomposition produced from H3A/EG4 integrated strain #27 was alsoincluded. Accellerase® 1500, Accellerase® DUET, Accellerase® BG,OPTIMASH™ BG, OPTIMASH™ TBG, and OPTIMASH™ VR were products availablefrom Danisco US Inc., Genencor.

Pretreated wheat straw as described above was used. The compositionanalysis was performed and is listed in Table 2 (see Example 17).

The saccharification process was performed by incubating the pretreatedwheat straw (25% dry matter) with various enzymes in reaction chambers.See, Larsen et al., The IBUS Process-Lignocellulosic Bioethanol Close toA commercial Reality, (2008) Chem. Eng. Tech. 31(5):765-772. Theexperimental conditions are shown in Tables 3 and 4. In each chamber,the total mass was 10 kg. The initial pH of the wheat straw was about3.50 and was adjusted by adding Na₂CO₃ to pH 5.0. Glucose concentrationwas measured over time and cellulose conversion was calculated.

TABLE 3 Viscosity Enzyme Experimental Cellulase Loading g/kg drycondition Enzymes mL/g cellulose matter 1 Accellerase ® 1500 batch 10.22 0 2 Accellerase ® DUET 0.15 0 3 Accellerase ® DUET 0.25 0 4Accellerase ® DUET + 0.15 6 Optimash ™ BG 5 Accellerase ® DUET + 0.15 6Optimash ™ TBG 6 Accellerase ® DUET + 0.15 6 Optimash ™ VR

TABLE 4 Cellulase Viscosity Experimental Loading Enzyme conditionEnzymes mL/g cellulose g/kg dry matter 7 Accellerase ® 1500 0.22 0(batch 1) 8 Accellerase ® 1500 0.22 0 (batch 2) 9 Accellerase ® DUET0.15 0 10 Accellerase ® DUET + 0.15 0.1 Accellerase ® BG 11Accellerase ® DUET + 0.15 6 Accellerase ® BG 12 H3A/Eg4#27 0.15 0

Experimental conditions 1-6 were conducted on the first day (“Day 1”),and experimental conditions 7-12 were conducted on the second day (“Day2”).

The glucose concentration was measured after 6 hour saccharification foreach experimental condition. Accellerase® DUET at 0.25 mL/g celluloseresulted in 40.8 g glucose/kg after 6-h saccharification. See FIG. 45.The glucose concentration for Accellerase® DUET+OPTIMASH BG (or TBG)(0.15+6) (i.e., 0.15 mL Accellerase® DUET/g cellulose+6 g OPTIMASH BG(or TBG)/kg dry matter) was similar to the glucose concentration forAccellerase® 1500 at 0.22 mL/g cellulose. See FIG. 45. The glucoseconcentration for Accellerase® DUET+Accellerase BG at 0.15+6 (i.e., 0.15mL Accellerase® DUET/g cellulose+6 g Accellerase BG/kg dry matter) wassimilar to the glucose concentration for Accellerase® 1500 at 0.22 mL/gcellulose and higher than the glucose concentration for Accellerase®DUET at 0.15 mL/g cellulose. See FIG. 45. High concentration ofAccellerase® BG was able to reduce the viscosity of the saccharificationreaction mixture. Using the enzyme composition produced from fermentingH3A/EG4 #27, at an amount of 0.15 mL/g cellulose yielded 37.5 g/kgglucose after 6-h saccharification, which was substantially higher thanthe glucose production for Accellerase® 1500 at 0.22 mL/g cellulose andAccellerase® DUET at 0.15 mL/g cellulose. See FIG. 45.

Glucose concentrations for various experimental conditions of Day 1'sexperiment were measured again after 24-h saccharification. See FIG. 46.The glucose concentration and cellulose conversion were measured overtime for experimental conditions 7-12 on Day 2's experiment and resultsare shown in FIGS. 47 and 48.

Viscosity was observed by eye on Day 1's experiment after 6-hsaccharification and is summarized in Table 6. More “+” indicates lessviscous saccharification reaction mixture. In general, less viscoussaccharification reaction mixture (e.g., thinner slurry) correlated withmore glucose production.

TABLE 6 Viscosity observation for Day 1's experiment at 6-h ExperimentalViscosity Glucose condition Enzymes Observation (g/kg) 1 Accellerase ®1500, 0.22 ++ 32.1 2 Accellerase ® DUET, 0.15 + 27 3 Accellerase ® DUET,0.25 ++++ 40.8 4 Accellerase ® DUET + Optimash ++ 31.4 BG 5Accellerase ® DUET + Optimash + 30.6 TBG 6 Accellerase ® DUET + Optimash+++ 26.7 VR

Viscosity of the saccharification reaction mixtures in various chamberson Day 2's experiment was observed by eye with reference to thevisibility of the metal parts in each chamber. After 6-day ofsaccharification at 50° C., the saccharification mixture in chamber 3(Experimental condition 9, Accellerase® DUET at 0.15 mL/g cellulose) wasmore viscous than the saccharification mixture in chamber 1(Experimental condition 7) or 2 (Experimental condition 8, Accellerase®1500 at 0.22 mL/g cellulose). Metal parts in chamber 3 could not beseen. The viscosity of the saccharification mixture in chamber 4(Experimental condition 10, Accellerase DUET® at 0.15 mL/gcellulose+Accellerase® BG at 0.1 g/kg dry matter) was reduced comparedto the viscosity of the saccharification mixture in chamber 3(Accellerase® DUET at 0.15 mL/g cellulose). The viscosity of thesaccharification mixture in chamber 5 (Experimental condition 11,Accellerase DUET® at 0.15 mL/g cellulose+Accellerase BG at 6 g/kg drymatter) was more reduced compared to the viscosity of thesaccharification mixture in chamber 4 (Accellerase® DUET at 0.15 mL/gcellulose+Accellerase BG at 0.1 g/kg dry matter). Even with a highamount of Accellerase BG, the saccharification mixture (chamber 5,Accellerase DUET® at 0.15 mL/g cellulose+Accellerase BG at 6 g/kg drymatter) was still more viscous than Accellerase® 1500 at 0.22 mL/gcellulose (chambers 1 and 2). However, with the addition of the enzymecomposition produced from fermenting H3A/EG4 #27, it was surprisinglyfound that the viscosity of the saccharification mixture (chamber 6) wassubstantially reduced compared to the viscosity of the saccharificationmixture in chamber 4 or 5. Metal parts in chamber 6 could be seen.

Example 21 Determining the Effects of Various Cellulases on ViscosityReduction and glucose production in saccharification process

A saccharification process was performed by incubating Inbiconpretreated wheat straw (25% dry matter) with various enzymes in reactionchambers. The experimental conditions are shown in Table 7. In eachchamber, the total mass is 10 kg. The initial pH of the wheat straw wasabout 3.50 and was adjusted by adding Na₂CO₃ to pH 5.0. Accellerase®1500, Accellerase® DUET, Accellerase® BG, Optimash™ BG, and Primafast®LUNA are products available from Genecor.

TABLE 7 Experimental Cellulase Loading Viscosity Enzyme conditionEnzymes mL/g cellulose g/kg dry matter 1 Accellerase ® DUET 0.15 0 2Accellerase ® 1500 0.22 0 3 Accellerase ® DUET + Optimash BG 0.15 1 4Accellerase ® DUET + Optimash BG 0.15 2 5 Accellerase ® DUET + PrimafastLUNA 0.15 1 6 Accellerase ® DUET + Primafast LUNA 0.15 2 7 Accellerase ®DUET + Accellerase ® BG 0.15 1 8 Accellerase ® DUET + Accellerase ® BG0.15 2 9 Accellerase ® DUET + Optimash BG + 0.15 1 for OptimashAccellerase ® BG BG; 1 for Accellerase ® BG 10 Accellerase ® DUET +Accellerase ® 1500 0.15 for Accellerase ® 0 DUET; 0.22 for Accellerase ®1500 11 H3A/Eg4#27 + Optimash BG 0.15 1 12 H3A/Eg4#27 + Optimash BG 0.152 13 H3A/Eg4#27 + Primafast Luna 0.15 1 14 H3A/Eg4#27 + Primafast Luna0.15 2 15 H3A/Eg4#27 + Accellerase ® BG 0.15 1 16 H3A/Eg4#27 +Accellerase ® BG 0.15 2

Glucose concentration was measured after 6 h, 24 h, 50 h, and 6 d ofsaccharification. Viscosity of saccharification reaction mixture wasobserved by eye and measured by a viscosity meter using methods known toone skilled in the art after 6 h, 24 h, 50 h, and 6 d ofsaccharification.

It was found that the glucose production of each of the experimentalconditions 3-16 was increased compared to the glucose production ofexperimental condition 1. It was further found that the viscosity ofeach of the experimental conditions 3-16 was reduced compared to theviscosity of experimental condition 1.

This study also examined the glucose production and viscosity reductionin a saccharification process with the same experimental conditions asabove but after a prolonged pre-hydrolysis time (such as 6 h, 9 h, 12 h,24 h).

Example 22 Ascorbic Acid Effect on Avicel Hydrolysis by CBH1 and EG4

Crystalline cellulose (50 μL of 10% Avicel in 50 mM Sodium Acetate, pH5.0) reactions were initiated by mixing together combinations ofpurified T. reesei CBH1 (5 mg/g final concentration), purified T. reeseiEg4 (10 mg/g final concentration), ascorbic acid (50 mM stock, 8.8 g/Lfinal concentration) and manganese solution (10 mM final concentration)as described listed in FIG. 39A. Fifty (50) mM sodium acetate buffer, pH5.0, was added to each sample to a final volume of 300 μL.

Reaction eppendorf tubes were vortexed and then placed in an Innova 44incubator (New Brunswick Scientific) at 50° C., 200 rpm. Fifty (50) μLsamples were taken from each tube at three time points (2.5, 4.5, 24 h)and quenched with 50 μL of 100 mM glycine buffer, pH 10.0. Samples werecentrifuged at 3000 rpm for 5 minutes (Rotanta 460R Centrifuge, HettichZentrifugen) and supernatant (20 μL) was added to 100 μL of water in anHPLC 96-well microtiter plate (Agilent, 5042-1385). Glucose andcellobiose concentrations were measured by HPLC using Aminex HPX-87Pcolumn (300 mm×7.8 mm, 125-0098) pre-fitted with guard column. Theresults are shown in FIG. 37.

Next ascorbic acid effect on Avicel hydrolysis by CBH2 and EG4 wasmeasured. Crystalline cellulose (80 μL of 10% Avicel in 50 mM SodiumAcetate, pH 5.0) reactions were initiated by mixing togethercombinations of purified T. reesei CBH2 (5 mg/g final concentration),purified T. reesei Eg4 (10 mg/g final concentration), ascorbic acid (50mM stock, 8.8 g/l final concentration) and manganese solution (10 mMfinal concentration) as listed in FIG. 39B. Fifty (50) mM sodium acetatebuffer, pH 5.0, was added to each sample to a final volume of 500 μL.

Reaction eppendorf tubes were vortexed and then placed in an Innova 44incubator (New Brunswick Scientific) at 50° C., 200 rpm. Fifty (50) μLsamples were taken from each tube at three time points (5, 24, 48 h) andquenched with 50 μL of 100 mM glycine buffer, pH 10.0. Samples werecentrifuged at 3000 rpm for 5 minutes (Rotanta 460R Centrifuge, HettichZentrifugen) and supernatant (20 μL) was added to 100 μL of water in anHPLC 96-well microtiter plate (Agilent, 5042-1385). Glucose andcellobiose concentrations were measured by HPLC using Aminex HPX-87Pcolumn (300 mm×7.8 mm, 125-0098) pre-fitted with guard column. Resultsare shown in FIG. 38.

1. A biomass saccharification mixture comprising: a. a biomass materialb. an enzyme composition comprising a glycosyl hydrolase family 61enzyme having endoglucanase activity, which is: i. at least 65% insequence identity to any one of SEQ ID NO:1-29 and 148; ii. at least 65%in sequence identity to residues 22-344 of SEQ ID NO:27 iii. comprisesat least one amino acid sequence motifs selected from the groupconsisting of: SEQ ID NOs: 84-91; iv. comprises one or more sequencemotifs selected from the group consisting of: (1) SEQ ID NO:84 and 88;(2) SEQ ID NOs: 85 and 88; (3) SEQ ID NO:86; (4) SEQ ID NO:87; (5) SE IDNO:84, 88 and 89; (6) SEQ ID NOs: 84, 88 and 91; (10) SEQ ID NOs: 85, 88and 91; (11) SEQ ID NOs: 84, 88, 89 and 91; (12) SEQ ID NOs: 84, 88, 90and 91; (13) SEQ ID NOs: 85, 88, 89 and 91; and (14) SEQ ID NOs: 85, 88,90 and 91; v. encoded by a polynucleotide sequence or a complementthereof that is at least 65% sequence identity to SEQ ID NO:30; or vi.encoded by a polynucleotide sequence that hybridizes under highstringency conditions to SEQ ID NO:30 or to a complement thereof;wherein said biomass saccharification mixture has a lower viscosity thana biomass saccharification mixture without the glycosyl hydrolyasefamily 61 enzyme and/or is capable of increasing the level ofsaccharification in the mixture as compared to the level ofsaccharification in a mixture having no or a lower level of glycosylhydrolase family 61 enzyme, wherein the level of saccharification ismeasured by the yield of fermentable sugar after the mixture isincubated for a period of time sufficient to cause saccharification ofthe biomass.
 2. (canceled)
 3. The biomass saccharification mixture ofclaim 1, wherein the glycosyl hydrolase family 61 enzyme is derived froma filamentous fungus; optionally wherein the filamentous fungus is oneselected from the group: Trichoderma, Humicola, Fusarium, Aspergillus,Neurospora, Penicillium, Cephalosporium, Achlva, Podospora, Endothia,Mucor, Cochliobolus, Pyricularia, Chrvsosporium, Aspergillus awamori,Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus,Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae,Chrysosporium lucknowense, Fusarium bactridioides, Fusarium cerealis,Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum,Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusariumoxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum,Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum,Fusarium torulosum, Fusarium trichothecioides, Fusarium venenatum,Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsis aneirina,Ceriporiopsis caregiea, Ceriporiopsis gilvescens, Ceriporiopsispannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa, Ceriporiopsissubvermispora, Coprinus cinereus, Coriolus hirsutus, Humicola insolens,Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila,Neurospora crassa, Neurospora intermedia, Penicillium purpurogenum,Penicillium canescens, Penicillium solitum, Penicillium funiculosumPhanerochaete chrysosporium, Phlebia radiate, Pleurotus ervngii,Talaromvces flavus, Thielavia terrestris, Trametes villosa, Trametesversicolor, Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, Trichoderma reesei, Trichoderma viride, Geosmithiaemersonii, or G. stearothermophilus. 4-7. (canceled)
 8. The biomasssaccharification mixture of claim 1, wherein the enzyme compositionfurther comprises one or more or all of: (1) a polypeptide havingxylanase activity, (2) a polypeptide having beta-xylosidase activity;(3) a polypeptide having L-alpha-arabinofuranosidase activity; and (4)at least one polypeptide having cellobiohydrolase activity and at leastone polypeptide having beta-glucosidase activity; optionally wherein: a.the polypeptide having xylanase activity is: i. a polypeptide encoding aT. reesei Xyn3 (SEQ ID NO:76), T. reesei Xyn2 (SEQ ID NO:77), an AfuXyn2(SEQ ID NO:58), and AfuXyn5 (SEQ ID NO:60), or a variant thereof havingat least 90% sequence identity thereto; or ii. a polypeptide encoded bya polynucleotide (1) having at least 90% sequence identity to SEQ IDNO:75, 57, or 59; or (2) hybridizes under high stringency conditions toSEQ ID NO: 75, 57, or 59, or to a complement thereof; b. the at leastone polypeptide having beta-xylosidase activity is: i. a polypeptideencoding an Fv3A (SEQ ID NO:36), an Fv43A (SEQ ID NO:44), a Pf43A (SEQID NO:38), an Fv43D (SEQ ID NO:62), an Fv39A (SEQ ID NO:42), an Fv43E(SEQ ID NO:40), an Fo43A (SEQ ID NO:52), an Fv43B (SEQ ID NO:46), aPa51A (SEQ ID NO:48), a Gz43A (SEQ ID NO:50), a T. reesei Bxl1 (SEQ IDNO:78), or a variant thereof having at least 90% sequence identitythereto; or ii. a polypeptide encoded by a polynucleotide (1) having atleast 90% sequence identity to SEQ ID NO:35, 43, 37, 61, 41, 39, 51, 45,47, 49, or 159; (2) hybridizes under high stringency conditions to SEQID NO: 35, 43, 37, 61, 41, 39, 51, 45, 47, 49, 159, or to a complementthereof; and/or c. the at least one polypeptide havingL-alpha-arabinofuranosidase activity is: i. a polypeptide encoding anAf43A (SEQ ID NO:54), an Fv43B (SEQ ID NO:46), a Pf51A (SEQ ID NO:56), aPa51A (SEQ ID NO:48), an Fv51A (SEQ ID NO:66), or a variant thereofhaving at least 90% sequence identity thereto; or ii. a polypeptideencoded by a polynucleotide (1) having at least 90% sequence identity toSEQ ID NO:53, 45, 55, 47, or 65; (2) hybridizes under high stringencyconditions to SEQ ID NO: 53, 45, 55, 47, or 65, or to a complementthereof; d. the at least one polypeptide having cellobiohydrolaseactivity is a polypeptide encoding a T. reesei CBH1, Af 7A (SEQ IDNO:150), Af7B (SEQ ID NO:151), Cg7A (SEQ ID NO:152), Cg7B (SEQ IDNO:153), Tt7A (SEQ ID NO:154), Tt7B (SEQ ID NO:155), T. reesei CBH2,Tt6A (SEQ ID NO:156), St6A (SEQ ID NO:157), St6B (SEQ ID NO:158), or avariant thereof having at least 90% sequence identity thereto; and/or e.the at least one polypeptide having beta-glucosidase activity is: i. apolypeptide encoding an Fv3C (SEQ ID NO:100), a Pa3D (SEQ ID NO:94), anFv3G (SEQ ID NO:96), an Fv3D (SEQ ID NO:98), a Tr3A (SEQ ID NO:102), aTr3B (SEQ ID NO:104), a Te3A (SEQ ID NO:106), an An3A (SEQ ID NO:108),an Fo3A (SEQ ID NO:110), a Gz3A (SEQ ID NO:112), an Nh3A (SEQ IDNO:114), a Vd3A (SEQ ID NO:116), a Pa3G (SEQ ID NO:118), a Tn3B (SEQ IDNO:119), or a variant thereof having at least 90% sequence identitythereto; or ii. a polypeptide encoded by a polynucleotide (1) having atleast 90% sequence identity to SEQ ID NO:99, 93, 95, 97, 101, 103, 105,107, 109, 111, 113, 115, or 117; (2) hybridizes under high stringencyconditions to SEQ ID NO: 99, 93, 95, 97, 101, 103, 105, 107, 109, 111,113, 115, or 117, or to a complement thereof. 9-11. (canceled)
 12. Thebiomass saccharification mixture of claim 1, wherein the enzymecomposition comprises (1) about 0.1 wt. % to about 50 wt. %, about 1 wt.% to about 20 wt. %, about 5 wt. % to about 15 wt. % of the polypeptidehaving GH61/endoglucanase activity, referencing the total weight ofproteins in the enzyme composition; or (2) about 0.2 mg to about 30 mg,about 0.2 mg to about 20 mg, about 0.5 mg to about 10 mg, or about 1 mgto about 5 mg of the polypeptide having GH61/endoglucanase activity pergram of cellulose, hemicelluloses or a mixture of cellulose andhemicelluloses contained in the biomass material.
 13. The biomasssaccharification mixture of claim 8, wherein the enzyme compositioncomprises cellobiohydrolase in an amount that is (1) about 0.1 wt. % toabout 80 wt. %, about 5 wt. % to about 70 wt. %, about 10 wt. % to about60 wt. %, about 20 wt. % to about 50 wt. %, or about 25 wt. % to about50 wt. % of the total weight of proteins in the enzyme composition; or(2) about 0.2 mg to about 30 mg, about 0.2 mg to about 20 mg, about 0.5mg to about 10 mg, or about 0.5 mg to about 5 mg per gram of cellulose,hemicelluloses, or a mixture of cellulose and hemicelluloses in thebiomass saccharification mixture; and comprises beta-glucosidase in anamount that is (1) about 0.1 wt. % to about 50 wt. %, about 1 wt. % toabout 30 wt. %, about 2 wt. % to about 20 wt. %, about 5 wt. % to about20 wt. %, or about 8 wt. % to about 15 wt. % of the total weight ofproteins in the enzyme composition; or (2) about 0.2 mg to about 30 mg,about 0.2 mg to about 20 mg, about 0.5 mg to about 10 mg, or about 0.5mg to about 5 mg per gram of cellulose, hemicelluloses, or a mixture ofcellulose and hemicelluloses in the biomass saccharification mixture.14. The biomass saccharification mixture of claim 8, wherein: a. theenzyme composition comprises (1) about 0.1 wt. % to about 50 wt. %,about 1 wt. % to about 40 wt. %, about 4 wt. % to about 30 wt. %, about5 wt. % to about 20 wt. %, or about 8 wt. % to about 15 wt. % of thepolypeptide having xylanase activity, referencing the total weight ofproteins in the enzyme composition; or (2) about 0.2 mg to about 30 mg,about 0.2 mg to about 20 mg, about 0.5 mg to about 10 mg, or about 0.5mg to about 5 mg of the polypeptide having xylanase activity per gram ofcellulose, hemicelluloses, or a mixture of cellulose and hemicellulosesin the biomass saccharification mixture; b. the enzyme compositioncomprises (1) about 0.1 wt. % to about 50 wt. %, about 1 wt. % to about40 wt. %, about 2 wt. % to about 30 wt. %, about 4 wt. % to about 20 wt.%, or about 5 wt. % to about 15 wt. % of the polypeptide havingbeta-xylosidase activity, referencing the total weight of proteins inthe enzyme composition; or (2) about 0.2 mg to about 30 mg, about 0.2 mgto about 20 mg, about 0.5 mg to about 10 mg, or about 0.5 mg to about 5mg of the polypeptide having beta-xylosidase activity per gram ofcellulose, hemicelluloses, or a mixture of cellulose and hemicellulosesin the biomass saccharification mixture; and/or c. the enzymecomposition comprises (1) about 0.1 wt. % to about 50 wt. %, about 0.1wt. % to about 50 wt. %, about 1 wt. % to about 40 wt. %, about 2 wt. %to about 30 wt. %, about 4 wt. % to about 20 wt. %, or about 5 wt. % toabout 15 wt. % of the polypeptide having L-alpha-arabinofuranosidaseactivity, referencing the total weight of proteins in the enzymecomposition; or (2) about 0.2 mg to about 30 mg, about 0.2 mg to about20 mg, about 0.5 mg to about 10 mg, or about 0.5 mg to about 5 mg of thepolypeptide having L-alpha-arabinofuranosidase activity per gram ofcellulose, hemicelluloses, or a mixture of cellulose and hemicellulosesin the biomass saccharification mixture. 15-16. (canceled)
 17. Thebiomass saccharification mixture of claim 1, wherein the enzymecomposition is a whole cellulase composition, wherein the wholecellulase composition is derived from a host cell expressing apolynucleotide encoding a polypeptide having GH61/endoglucanaseactivity, optionally wherein the polynucleotide encoding the polypeptidehaving GH61 family enzyme activity is heterologous to the host cell.18-21. (canceled)
 22. The biomass saccharification mixture of claim 17,wherein the whole cellulase composition is derived from a host cellexpressing one or more or all of (1) a polynucleotide encoding a peptidehaving beta-xylosidase activity; (2) a polynucleotide encoding apolypeptide having xylanase activity; and (3) a polynucleotide peptidehaving L-alpha-arabinofuranosidase activity; (4) a polynucleotideencoding a polypeptide having cellobiohydrolase activity; and (5) apolynucleotide encoding a polypeptide having beta-glucosidase activity,optionally wherein the polynucleotide of one or more or all of (1) to(5) is heterologous to the host cell. 23-24. (canceled)
 25. The biomasssaccharification mixture of claim 22, wherein one or more or all of: (1)the gene encoding the polypeptide having GH61/endoglucanase activity;(2) the gene encoding the polypeptide having cellobiohydrolase activity;(3) the gene encoding the polypeptide having beta-glucosidase activity;(4) the gene encoding the polypeptide having beta-xylosidase activity;(5) the gene encoding the polypeptide having xylanase activity; and (6)the gene encoding the polypeptide having L-alpha-arabinofuranosidaseactivity are integrated into the genetic material of the host cell. 26.The biomass saccharification mixture of claim 17, wherein the host cellis a bacterial host cell, yeast host cell, or a fungal host cell,optionally wherein the host cell is a filamentous fungal host cell, andoptionally wherein the filamentous fungal host cell is one selected froma cell of Aspergillus niger, Aspergillus oryzae, Chrysosporiumlucknowense, Trichoderma reesei, Aspergillus awamori, Aspergillusfumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillusnidulans, Fusarium bactridioides, Fusarium cerealis, Fusariumcrookwellense, Fusarium culmorum, Fusarium graminearum, Fusariumgraminum, Fusarium heterosporum, Fusarium negundi, Fusarium oxysporum,Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusariumsarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusariumtorulosum, Fusarium trichothecioides, Fusarium venenatum, Bierkanderaadusta, Ceriporiopsis aneirina, Ceriporiopsis aneirina, Ceriporiopsiscaregiea, Ceriporiopsis gilvescens, Ceriporiopsis pannocinta,Ceriporiopsis rivulosa, Ceriporiopsis subrufa, Ceriporiopsissubvermispora, Coprinus cinereus, Coriolus hirsutus, Humicola insolens,Humicola lanuginosa, Mucor miehei, Mvceliophthora thermophile,Neurospora crassa, Neurospora intermedia, Penicillium purpurogenum,Penicillium canescens, Penicillium solitum, Penicillium funiculosumPhanerochaete chrysosporium, Phlebia radiate, Pleurotus eryngii,Talaromyces flavus, Thielavia terrestris, Trametes villosa, Trametesversicolor, Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, or Trichoderma viride. 27-28. (canceled)
 29. Thebiomass saccharification mixture of claim 1, wherein thesaccharification mixture is prepared by first blending the enzymecomposition comprising the polypeptide having GH61/endoglucanaseactivity, followed by mixing the enzyme composition with the biomass.30-31. (canceled)
 32. The biomass saccharification mixture of claim 1,wherein the biomass material is selected from seeds, grains, tubers,plant waste, byproducts of food processing or industrial processing,corn cobs, corn stover, grasses, Sorghastrum nutans, switchgrass,perennial canes, wood, wood chips, wood processing waste, sawdust,paper, paper waste, pulp, and recycled paper, potatoes, soybean, barley,rye, oats, wheat, beets, sugar cane bagasse and straw.
 33. The biomasssaccharification mixture of claim 1, wherein the biomass material issubjected to pretreatment with an acid or a base, optionally wherein thepretreated biomass is adjusted to pH of about 4.0 to 6.5 before mixingwith the enzyme composition.
 34. 35. The biomass saccharificationmixture of claim 1, wherein the biomass material is present in themixture in an amount of about 5 wt. % to about 60 wt. %, about 10 wt. %to about 50 wt. %, about 15 wt. % to about 40 wt. %, about 15 wt. % toabout 30 wt. %, or about 20 wt. % to about 30 wt. %, referring to theamount of biomass material in its solid state relative to the totalweight of the mixture.
 36. A method of hydrolyzing a biomass materialcomprising incubating the biomass saccharification mixture of claim 1,under conditions suitable for hydrolyzing the biomass materials in thebiomass saccharification mixture and for a sufficient period of time.37. The method of claim 36, wherein the conditions suitable forhydrolyzing the biomass materials in the biomass saccharificationmixture comprises: (1) a pH of about 3.5 to about 7.0; (2) for aduration of about 2 hours or longer; and/or (3) a temperature of about20° C. to about 75° C.
 38. (canceled)
 39. The method of claim 36,wherein at any given time above 2 hours, the amount of fermentablesugars is produced by the biomass saccharification mixture is increasedby at least about 5% or at least about 10% as compared to the amount offermentable sugars produced by a control biomass saccharificationmixture comprising the same amount and type of biomass material, and thesame composition of enzyme components but in the absence of theGH61/endoglucanase.
 40. (canceled)
 41. The method of claim 36, whereinthe biomass material is present in an amount of about 10 wt. % to about50 wt. % in its solid state.
 42. The method of claim 41, wherein theviscosity of the biomass saccharification mixture is reduced by at leastabout 5%, about 10%, about 15%, about 20%, about 25%, or more, ascompared to the viscosity of the control biomass saccharificationmixture comprising the same amount and type of biomass material, and thesame composition of enzyme components but in the absence of theGH61/endoglucanase.
 43. A method of using the composition of claim 1 toconvert a biomass material into fermentable sugars in a merchant enzymesupply model or an on-site bio-refinery model.